# HG changeset patch # User workflow4metabolomics # Date 1664554736 0 # Node ID 77abacd33c31d727a5b958ee3ac5f41b69a7934e # Parent 78d5a12406c2d06651d744ff503a415e931b2f04 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 diff -r 78d5a12406c2 -r 77abacd33c31 MS2snoop.R --- a/MS2snoop.R Fri Aug 05 17:25:45 2022 +0000 +++ b/MS2snoop.R Fri Sep 30 16:18:56 2022 +0000 @@ -1,1236 +1,1233 @@ -#' -#' read and process mspurity W4M files -#' create a summary of fragment for each precursor and a graphics of peseudo -#' spectra + correlation on which checking of fragment is based on -#' V3 try to identify and process multiple files for 1 precursor which may -#' occur if different collision energy are used -#' V4 elimination of correlation = NA. Correlation is done with precursor, if -#' precursor is not present correlation with most intense peak -#' author: Jean-Francois Martin -#' V5 is versionned, lintR-compliant, packaged, unit-tested, documented and -#' tested against data from other labs. -#' new maintainer: Lain Pavot - lain.pavot@inrae.fr -#' -#' @import optparse -#' - - -get_version <- function() { - cmd <- commandArgs(trailingOnly = FALSE) - root <- dirname(gsub("--file=", "", cmd[grep("--file=", cmd)])) - readme <- readLines(file.path(root, "README.md")) - version_line <- readme[grepl(" * **@version**: ", readme, fixed = TRUE)] - return(gsub(".*: ", "", version_line)) -} - -defaults <- list( - MS2SNOOP_VERSION = get_version(), - MISSING_PARAMETER_ERROR = 1, - BAD_PARAMETER_VALUE_ERROR = 2, - MISSING_INPUT_FILE_ERROR = 3, - NO_ANY_RESULT_ERROR = 255, - DEFAULT_PRECURSOR_PATH = NULL, - DEFAULT_FRAGMENTS_PATH = NULL, - DEFAULT_COMPOUNDS_PATH = NULL, - DEFAULT_OUTPUT_PATH = "compound_fragments_result.txt", - DEFAULT_TOLMZ = 0.01, - DEFAULT_TOLRT = 20, - DEFAULT_MZDECIMAL = 3, - DEFAULT_R_THRESHOLD = 0.85, - DEFAULT_MINNUMBERSCAN = 8, - DEFAULT_SEUIL_RA = 0.05, - DEFAULT_FRAGMENTS_MATCH_DELTA = 10, - DEFAULT_FRAGMENTS_MATCH_DELTA_UNIT = "ppm", - DEFAULT_PDF_PATH = "" -) -env <- globalenv() -for (default in names(defaults)) { - assign(default, defaults[[default]], envir = env) - lockBinding(default, env) -} - -######################################################################## - -get_formulas <- function( - mzref, - spectra, - nominal_mz_list, - processing_parameters, - background = !TRUE -) { - if (is.vector(mzref) && length(mzref) > 1) { - return(lapply( - mzref, - function(mz) { - return(get_formulas( - mzref = mz, - spectra = spectra, - nominal_mz_list = nominal_mz_list, - processing_parameters = processing_parameters, - background = background - )) - } - )) - } - input <- sprintf( - "%s-%s.ms", - gsub("[[:space:]]", "_", processing_parameters$c_name), - mzref - ) - create_ms_file(input, mzref, spectra, processing_parameters) - output <- sprintf( - "out/%s-%s.out", - gsub("[[:space:]]", "_", processing_parameters$c_name), - mzref - ) - command <- sprintf( - paste( - "sirius", - "--noCite", - "--noSummaries", - "--loglevel=WARNING", - "-i='%s'", - "-o='%s'", - "tree", - ## loglevel is not working taken into account during - ## sirius startup, so we filter outputs... - "2>&1 | grep '^(WARNING|SEVERE)'" - ), - input, - output - ) - verbose_catf( - ">> Sirius is running %swith the command: %s\n", - if (background) "in the background " else "", - command - ) - system( - command, - wait = !background, - ignore.stdout = background, - ignore.stderr = background - ) - return(extract_sirius_results(output, spectra$mz, processing_parameters)) -} - -create_ms_file <- function( - path, - mzref, - spectra, - processing_parameters -) { - file_content <- paste( - sprintf(">compound %s", processing_parameters$c_name), - sprintf(">ionization %s", processing_parameters$ionization), - sprintf(">parentmass %s", mzref), - sprintf(">formula %s", processing_parameters$elemcomposition), - sep = "\n" - ) - displayed_file_content <- sprintf( - "%s\n>collision\n%s", - file_content, - paste( - sprintf( - "%s %s", - spectra[1:3, "mz"], - spectra[1:3, "intensities"] - ), - collapse = "\n" - ) - ) - if (nrow(spectra) > 3) { - displayed_file_content <- sprintf( - "%s\n[... %s more rows of mz and intensities ...]", - displayed_file_content, - nrow(spectra) - 3 - ) - } - catf( - ">> MS file created for %s with content:\n%s\n", - processing_parameters$c_name, - displayed_file_content - ) - file_content <- sprintf( - "%s\n\n>collision\n%s", - file_content, - paste( - sprintf("%s %s", spectra$mz, spectra$intensities), - collapse = "\n" - ) - ) - cat(file_content, file = path, append = FALSE) -} - -extract_sirius_results <- function( - output, - mz_list, - processing_parameters -) { - - delta <- processing_parameters$fragment_match_delta - delta_unit <- tolower(processing_parameters$fragment_match_delta_unit) - - output <- list.dirs(output, recursive = FALSE)[[1]] - - spectra_out_dir <- sprintf("%s/spectra", output) - spectra_filename <- sprintf( - "%s/%s", - spectra_out_dir, - list.files(spectra_out_dir)[[1]] - ) - - trees_out_dir <- sprintf("%s/trees", output) - trees_filename <- sprintf( - "%s/%s", - trees_out_dir, - list.files(trees_out_dir)[[1]] - ) - - if (!is.null(spectra_filename)) { - sirius_results <- get_csv_or_tsv(spectra_filename) - } else { - return(rep(NA, length(mz_list))) - } - if (!is.null(trees_filename)) { - sirius_results <- cbind(sirius_results, extract_sirius_ppm(trees_filename)) - } else { - return(rep(NA, length(mz_list))) - } - - fragment_matchings <- data.frame( - formula = NA, - ppm = NA, - mz = mz_list, - error = NA - ) - - sirius_results <- filter_sirius_with_delta( - sirius_results = sirius_results, - original_mz = fragment_matchings$mz, - delta = delta, - delta_unit = delta_unit - ) - - for (index in seq_len(nrow(sirius_results))) { - result <- sirius_results[index, ] - filter <- which(order(abs(fragment_matchings$mz - result$mz)) == 1) - fragment_matchings[filter, "formula"] <- result$formula - fragment_matchings[filter, "ppm"] <- result$ppm - catf( - "[OK] Fragment with m/z=%s matches %s with a difference of %s ppm\n", - fragment_matchings[filter, "mz"], result$formula, result$ppm - ) - } - return(fragment_matchings) -} - -filter_sirius_with_delta <- function( - sirius_results, - original_mz, - delta, - delta_unit -) { - if (is.numeric(delta) && !is.na(delta) && delta > 0) { - if (delta_unit == "ppm") { - filter <- abs(sirius_results$ppm) <= delta - fine <- which(filter) - not_fine <- which(!filter) - catf( - paste("[KO] fragment %s (m/z=%s) eleminated because ppm=%s is greater", - "than delta=%s\n" - ), - sirius_results[not_fine, ]$formula, - sirius_results[not_fine, ]$mz, - sirius_results[not_fine, ]$ppm, - delta - ) - sirius_results <- sirius_results[fine, ] - } else if (delta_unit == "mz") { - differences <- sapply( - sirius_results$mz, - function(mz) min(abs(original_mz - mz)) - ) - fine <- which(sapply( - sirius_results$mz, - function(mz) any(abs(original_mz - mz) <= delta) - )) - not_fine <- which(sapply( - sirius_results$mz, - function(mz) all(abs(original_mz - mz) > delta) - )) - catf( - paste( - "[KO] fragment %s eleminated because mz difference=%s is", - "greater than delta=%s\n" - ), - sirius_results[not_fine, ]$formula, - differences[not_fine], - delta - ) - sirius_results <- sirius_results[fine, ] - } - } - return(sirius_results) -} - -extract_sirius_ppm <- function(path) { - json <- file(path, "r") - suppressWarnings(json_lines <- readLines(json)) - close(json) - json_lines <- json_lines[ - grepl("\\s+\"(massDeviation|recalibratedMass)\" :", json_lines) - ] - json_lines <- gsub("^\\s+\"[^\"]+\" : \"?", "", json_lines) - ppms <- json_lines[seq(1, length(json_lines), 2)] - mz <- json_lines[seq(2, length(json_lines), 2)] - ppms <- as.numeric(gsub(" ppm .*", "", ppms)) - mz <- as.numeric(gsub(",$", "", mz)) - ordered <- order(mz) - return(list(ppm = ppms[ordered], recalibrated_mz = mz[ordered])) -} - -#' @title plot_pseudo_spectra -#' @param x -#' @param fid -#' @param sum_int -#' @param vmz -#' @param cor_abs_int -#' @param refcol -#' @param c_name -#' @description plot_pseudo_spectra -#' function to compute sum of intensities among scans for all -#' m/z kept (cor > r_threshold & minimum number of scans) -#' and plot pseudo spectra -#' x dataframe scan X fragments with scans number in the 1st column and -#' ions in next with intensities -#' fid file id when several a precursor has been detected in several files -plot_pseudo_spectra <- function( - x, - fid, - sum_int, - vmz, - cor_abs_int, - refcol, - meaned_mz, - processing_parameters -) { - ## du fait de la difference de nombre de colonne entre la dataframe qui - ## inclue les scans en 1ere col, mzRef se decale de 1 - refcol <- refcol - 1 - ## compute relative intensities max=100% - rel_int <- sum_int[-1] - rel_int <- rel_int / max(rel_int) - - if (processing_parameters$do_pdf) { - ## define max value on vertical axis (need to increase in order to plot the - ## label of fragments) - ymax <- max(rel_int) + 0.2 * max(rel_int) - - par(mfrow = c(2, 1)) - plot(vmz, rel_int, type = "h", ylim = c(0, ymax), - main = processing_parameters$c_name - ) - ## low correl coef. will be display in grey - cor_low <- which(round(cor_abs_int, 2) < processing_parameters$r_threshold) - - lbmzcor <- sprintf("%s(r=%s)", vmz, round(cor_abs_int, 2)) - - if (length(cor_low) > 0) { - text( - vmz[cor_low], - rel_int[cor_low], - lbmzcor[cor_low], - cex = 0.5, - col = "grey", - srt = 90, - adj = 0 - ) - if (length(vmz) - length(cor_low) > 1) { - text( - vmz[-c(refcol, cor_low)], - rel_int[-c(refcol, cor_low)], - lbmzcor[-c(refcol, cor_low)], - cex = 0.6, - col = 1, - srt = 90, - adj = 0 - ) - } - } else { - if (length(vmz) > 1) { - text( - vmz[-c(refcol)], - rel_int[-c(refcol)], - lbmzcor[-c(refcol)], - cex = 0.6, - col = 1, - srt = 90, - adj = 0 - ) - } - } - - text( - vmz[refcol], - rel_int[refcol], - lbmzcor[refcol], - cex = 0.8, - col = 2, - srt = 90, - adj = 0 - ) - } - - ## prepare result file - cor_valid <- (round(cor_abs_int, 2) >= processing_parameters$r_threshold) - - do_sirius <- TRUE - verbose_catf("Checking sirius parameters...\n") - if (is.null(processing_parameters$ionization)) { - do_sirius <- FALSE - verbose_catf("[KO] No ionization passed in parameter.\n") - } else { - verbose_catf("[OK] Ionization=%s.\n", processing_parameters$ionization) - } - if (is.na(processing_parameters$elemcomposition)) { - do_sirius <- FALSE - verbose_catf("[KO] Elemental composition is NA.\n") - } else if (length(processing_parameters$elemcomposition) < 1) { - do_sirius <- FALSE - verbose_catf("[KO] No elemental composition is provided.\n") - } else if (processing_parameters$elemcomposition == "") { - do_sirius <- FALSE - verbose_catf("[KO] Elemental composition is an empty string.\n") - } else { - verbose_catf( - "[OK] Elemental composition=%s.\n", - processing_parameters$elemcomposition - ) - } - - cp_res_length <- length(vmz) - ppm <- rep(NA, cp_res_length) - formulas <- rep(NA, cp_res_length) - if (do_sirius) { - verbose_catf("Everything is ok, preparing for sirius.\n") - formulas <- get_formulas( - mzref = processing_parameters$mzref, - spectra = data.frame(mz = meaned_mz, intensities = sum_int[-1]), - nominal_mz_list = vmz, - processing_parameters = processing_parameters - ) - if (nrow(formulas) == 0) { - catf("No formula found.\n") - } else { - ppm <- formulas$ppm - formulas <- formulas$formula - catf( - "Found %s formula for %s fragments\n", - length(formulas[which(!(is.na(formulas)))]), - cp_res_length - ) - } - } else { - verbose_catf("Sirius cannot be run.\n") - } - cp_res <- data.frame( - rep(processing_parameters$c_name, cp_res_length), - rep(processing_parameters$inchikey, cp_res_length), - rep(processing_parameters$elemcomposition, cp_res_length), - formulas, - vmz, - ppm, - rep(fid, cp_res_length), - cor_abs_int, - sum_int[-1], - rel_int, - cor_valid - ) - - colnames(cp_res) <- c( - "compoundName", - "inchikey", - "elemcomposition", - "fragment", - "fragment_mz", - "ppm", - "fileid", - "CorWithPrecursor", - "AbsoluteIntensity", - "relativeIntensity", - "corValid" - ) - return(cp_res) -} - -#' -#' @title extract_fragments -#' -#' @param precursors the precursor list from mspurity -#' @param fragments the fragments list from ms purity -# ' @param mzref -# ' @param rtref -# ' @param c_name -# ' @param inchikey -# ' @param elemcomposition -#' @param processing_parameters -#' @returns -#' -#' @description -#' function for extraction of fragments corresponding to precursors -#' detected by MSPurity -extract_fragments <- function( ## nolint cyclocomp_linter - precursors, - fragments, - processing_parameters -) { - ## filter precursor in the precursors file based on mz and rt in the - ## compound list - catf("processing %s\n", processing_parameters$c_name) - verbose_catf("===\n") - param <- processing_parameters - selected_precursors <- which( - (abs(precursors$precurMtchMZ - param$mzref) <= param$tolmz) - & (abs(precursors$precurMtchRT - param$rtref) <= param$tolrt) - ) - rm(param) - - verbose_catf( - "> %s precursors selected with mz=%s±%s and rt=%s±%s\n", - length(selected_precursors), - processing_parameters$mzref, - processing_parameters$tolmz, - processing_parameters$rtref, - processing_parameters$tolrt - ) - - ## check if there is the precursor in the file - - if (length(selected_precursors) < 1) { - cat("> non detected in precursor file\n") - show_end_processing() - return(NULL) - } - - precursors <- precursors[selected_precursors, ] - - ## check if fragments corresponding to precursor are found in several - ## files (collision energy) - ## this lead to a processing for each fileid - file_ids <- as.character(sort(unique(precursors$fileid))) - if (length(file_ids) > 1) { - catf("> several files detected for this compounds :\n") - } else if (length(file_ids) < 1 || nrow(precursors) < 1) { - return(data.frame()) - } - - res_comp <- data.frame() - for (curent_file_id in file_ids) { - curent_precursors <- precursors[precursors$fileid == curent_file_id, ] - selected_fragments <- fragments[ - fragments$grpid %in% as.character(curent_precursors$grpid) - & fragments$fileid == curent_file_id, - ] - filtered_fragments <- selected_fragments[ - selected_fragments$ra > processing_parameters$seuil_ra, - ] - if (nrow(filtered_fragments) != 0) { - res_comp_by_file <- process_file( - curent_file_id = curent_file_id, - precursor_mz = curent_precursors$mz, - filtered_fragments = filtered_fragments, - processing_parameters = processing_parameters - ) - if (!is.null(res_comp_by_file)) { - res_comp <- rbind(res_comp, res_comp_by_file) - } - } else { - catf("No fragment found for in fragment file\n") - } - } - return(unique(res_comp)) -} - -process_file <- function( - curent_file_id, - precursor_mz, - filtered_fragments, - processing_parameters -) { - mznominal <- round(x = filtered_fragments$mz, digits = 0) - meaned_mz <- round( - aggregate( - data.frame( - mz = filtered_fragments$mz, - mznominal = mznominal - ), - list(mznominal), - FUN = mean - )$mz, - digits = processing_parameters$mzdecimal - ) - filtered_fragments <- data.frame(filtered_fragments, mznominal) - - ## creation of cross table row=scan col=mz X=ra - - vmz <- as.character(sort(unique(filtered_fragments$mznominal))) - - ds_abs_int <- create_ds_abs_int(vmz, filtered_fragments) - - if (global_debug) { - print(ds_abs_int) - } - - ## elimination of mz with less than min_number_scan scans (user defined - ## parameter) - xmz <- rep(NA, ncol(ds_abs_int) - 1) - sum_int <- rep(NA, ncol(ds_abs_int)) - nbxmz <- 0 - nb_scan_check <- min(nrow(ds_abs_int), processing_parameters$min_number_scan) - - for (j in 2:ncol(ds_abs_int)) { - sum_int[j] <- sum(ds_abs_int[j], na.rm = TRUE) - if (sum(!is.na(ds_abs_int[[j]])) < nb_scan_check) { - nbxmz <- nbxmz + 1 - xmz[nbxmz] <- j - } - } - - xmz <- xmz[-which(is.na(xmz))] - if (length(xmz) > 0) { - ds_abs_int <- ds_abs_int[, -c(xmz)] - sum_int <- sum_int[-c(xmz)] - ## liste des mz keeped decale de 1 avec ds_abs_int - vmz <- as.numeric(vmz[-c(xmz - 1)]) - meaned_mz <- meaned_mz[-c(xmz - 1)] - } - - ## mz of precursor in data precursor to check correlation with - mz_prec <- paste0( - "mz", - round(mean(precursor_mz), processing_parameters$mzdecimal) - ) - ## reference ion for correlation computing = precursor OR maximum - ## intensity ion in precursor is not present - refcol <- which(colnames(ds_abs_int) == mz_prec) - if (length(refcol) == 0) { - refcol <- which(sum_int == max(sum_int, na.rm = TRUE)) - } - - if (processing_parameters$do_pdf) { - start_pdf(processing_parameters, curent_file_id) - } - - ## Pearson correlations between absolute intensities computing - cor_abs_int <- rep(NA, length(vmz)) - - if (length(refcol) > 0) { - for (i in 2:length(ds_abs_int)) { - cor_abs_int[i - 1] <- stats::cor( - x = ds_abs_int[[refcol]], - y = ds_abs_int[[i]], - use = "pairwise.complete.obs", - method = "pearson" - ) - debug_catf( - "Correlation between %s and %s: %s\n", - paste(ds_abs_int[[refcol]], collapse = ";"), - paste(ds_abs_int[[i]], collapse = ";"), - paste(cor_abs_int[i - 1], collapse = ";") - ) - if (processing_parameters$do_pdf) { - pdf_plot_ds_abs_int( - processing_parameters$c_name, - ds_abs_int, - refcol, - i, - round(cor_abs_int[i - 1], 2) - ) - } - } - ## plot pseudo spectra - res_comp_by_file <- plot_pseudo_spectra( - x = ds_abs_int, - fid = curent_file_id, - sum_int = sum_int, - vmz = vmz, - cor_abs_int = cor_abs_int, - refcol = refcol, - meaned_mz = meaned_mz, - processing_parameters = processing_parameters - ) - catf( - "%s has been processed and %s fragments have been found.\n", - processing_parameters$c_name, - nrow(res_comp_by_file) - ) - } else { - res_comp_by_file <- NULL - cat(">> non detected in fragments file \n") - } - show_end_processing() - if (processing_parameters$do_pdf) { - end_pdf() - } - return(res_comp_by_file) -} - -create_ds_abs_int <- function(vmz, filtered_fragments) { - verbose_catf( - ">> fragments: %s\n", - paste(vmz, collapse = " ") - ) - ds_abs_int <- create_int_mz(vmz[1], filtered_fragments) - for (mz in vmz[-1]) { - int_mz <- create_int_mz(mz, filtered_fragments) - ds_abs_int <- merge( - x = ds_abs_int, - y = int_mz, - by.x = 1, - by.y = 1, - all.x = TRUE, - all.y = TRUE - ) - } - return(ds_abs_int) -} - -create_int_mz <- function(mz, filtered_fragments) { - ## absolute intensity - int_mz <- filtered_fragments[ - filtered_fragments$mznominal == mz, - c("acquisitionNum", "i") - ] - colnames(int_mz)[2] <- paste0("mz", mz) - ## average intensities of mass in duplicate scans - comp_scans <- aggregate(x = int_mz, by = list(int_mz[[1]]), FUN = mean) - return(comp_scans[, -1]) -} - -show_end_processing <- function() { - verbose_catf("==========\n") - cat("\n") -} - -start_pdf <- function(processing_parameters, curent_file_id) { - if (!dir.exists(processing_parameters$pdf_path)) { - dir.create(processing_parameters$pdf_path, recursive = TRUE) - } - pdf( - file = sprintf( - "%s/%s_processing_file%s.pdf", - processing_parameters$pdf_path, - processing_parameters$c_name, - curent_file_id - ), - width = 8, - height = 11 - ) - par(mfrow = c(3, 2)) -} - -pdf_plot_ds_abs_int <- function(c_name, ds_abs_int, refcol, i, r_coef) { - plot( - ds_abs_int[[refcol]], - ds_abs_int[[i]], - xlab = colnames(ds_abs_int)[refcol], - ylab = colnames(ds_abs_int)[i], - main = sprintf( - "%s corr coeff r=%s", c_name, r_coef - ) - ) -} -end_pdf <- function() { - dev.off() -} - -set_global <- function(var, value) { - assign(var, value, envir = globalenv()) -} - -set_debug <- function() { - set_global("global_debug", TRUE) -} - -unset_debug <- function() { - set_global("global_debug", FALSE) -} - -set_verbose <- function() { - set_global("global_verbose", TRUE) -} - -unset_verbose <- function() { - set_global("global_verbose", FALSE) -} - -verbose_catf <- function(...) { - if (global_verbose) { - cat(sprintf(...), sep = "") - } -} - - -debug_catf <- function(...) { - if (global_debug) { - cat(sprintf(...), sep = "") - } -} - -catf <- function(...) { - cat(sprintf(...), sep = "") -} - -create_parser <- function() { - parser <- optparse::OptionParser() - parser <- optparse::add_option( - parser, - c("-v", "--verbose"), - action = "store_true", - default = FALSE, - help = paste( - "[default %default]", - "Print extra output" - ) - ) - parser <- optparse::add_option( - parser, - c("-V", "--version"), - action = "store_true", - default = FALSE, - help = "Prints version and exits" - ) - parser <- optparse::add_option( - parser, - c("-d", "--debug"), - action = "store_true", - default = FALSE, - help = paste( - "[default %default]", - "Print debug outputs" - ) - ) - parser <- optparse::add_option( - parser, - c("-o", "--output"), - type = "character", - default = DEFAULT_OUTPUT_PATH, - action = "store", - help = "Path to the output file [default %default]" - ) - parser <- optparse::add_option( - parser, - c("-p", "--precursors"), - type = "character", - default = DEFAULT_PRECURSOR_PATH, - action = "store", - help = "Path to the precursors file [default %default]" - ) - parser <- optparse::add_option( - parser, - c("-f", "--fragments"), - type = "character", - default = DEFAULT_FRAGMENTS_PATH, - action = "store", - help = "Path to the fragments file [default %default]" - ) - parser <- optparse::add_option( - parser, - c("-c", "--compounds"), - type = "character", - default = DEFAULT_COMPOUNDS_PATH, - action = "store", - help = "Path to the compounds file [default %default]" - ) - parser <- optparse::add_option( - parser, - c("--tolmz"), - type = "numeric", - action = "store", - default = DEFAULT_TOLMZ, - metavar = "number", - help = paste( - "[default %default]", - "Tolerance for MZ (in Dalton) to match the standard in the compounds" - ) - ) - parser <- optparse::add_option( - parser, - c("--tolrt"), - type = "integer", - action = "store", - default = DEFAULT_TOLRT, - metavar = "number", - help = paste( - "[default %default]", - "RT (in seconds) to match the standard in the compounds" - ) - ) - parser <- optparse::add_option( - parser, - c("--seuil_ra"), - type = "numeric", - action = "store", - default = DEFAULT_SEUIL_RA, - metavar = "number", - help = paste( - "[default %default]", - "relative intensity threshold" - ), - ) - parser <- optparse::add_option( - parser, - c("--mzdecimal"), - type = "integer", - default = DEFAULT_MZDECIMAL, - action = "store", - help = paste( - "[default %default]", - "Number of decimal to write for MZ" - ), - metavar = "number" - ) - parser <- optparse::add_option( - parser, - c("--r_threshold"), - type = "integer", - default = DEFAULT_R_THRESHOLD, - action = "store", - help = paste( - "[default %default]", - "R-Pearson correlation threshold between precursor and fragment", - "absolute intensity" - ), - metavar = "number" - ) - parser <- optparse::add_option( - parser, - c("--min_number_scan"), - type = "numeric", - action = "store", - default = DEFAULT_MINNUMBERSCAN, - help = paste( - "[default %default]", - "Fragments are kept if there are found in a minimum number", - "of min_number_scan scans" - ), - metavar = "number" - ) - parser <- optparse::add_option( - parser, - c("--pdf_path"), - type = "character", - default = DEFAULT_PDF_PATH, - help = paste( - "[default %default]", - "PDF files output path" - ) - ) - parser <- optparse::add_option( - parser, - c("--ionization"), - type = "character", - action = "store", - default = "None", - help = paste( - "[default %default]", - "Which ionization to use for sirius" - ), - metavar = "character" - ) - parser <- optparse::add_option( - parser, - c("--fragment_match_delta"), - type = "numeric", - action = "store", - default = DEFAULT_FRAGMENTS_MATCH_DELTA, - help = paste( - "[default %default]", - "Fragment match delta" - ), - metavar = "numeric" - ) - parser <- optparse::add_option( - parser, - c("--fragment_match_delta_unit"), - type = "character", - action = "store", - default = DEFAULT_FRAGMENTS_MATCH_DELTA_UNIT, - help = paste( - "[default %default]", - "Fragment match delta" - ), - metavar = "character" - ) - return(parser) -} - -stop_with_status <- function(msg, status) { - sink(stderr()) - message(sprintf("Error: %s", msg)) - message(sprintf("Error code: %s", status)) - sink(NULL) - base::quit(status = status) -} - -check_args_validity <- function(args) { ## nolint cyclocomp_linter - if (length(args$output) == 0 || nchar(args$output[1]) == 0) { - stop_with_status( - "Missing output parameters. Please set it with --output.", - MISSING_PARAMETER_ERROR - ) - } - if (length(args$precursors) == 0 || nchar(args$precursors[1]) == 0) { - stop_with_status( - "Missing precursors parameters. Please set it with --precursors.", - MISSING_PARAMETER_ERROR - ) - } - if (length(args$fragments) == 0 || nchar(args$fragments[1]) == 0) { - stop_with_status( - "Missing fragments parameters. Please set it with --fragments.", - MISSING_PARAMETER_ERROR - ) - } - if (length(args$compounds) == 0 || nchar(args$compounds[1]) == 0) { - stop_with_status( - "Missing compounds parameters. Please set it with --compounds.", - MISSING_PARAMETER_ERROR - ) - } - if (!file.exists(args$precursors)) { - stop_with_status( - sprintf( - "Precursors file %s does not exist or cannot be accessed.", - args$precursors - ), - MISSING_INPUT_FILE_ERROR - ) - } - if (!file.exists(args$fragments)) { - stop_with_status( - sprintf( - "Fragments file %s does not exist or cannot be accessed.", - args$fragments - ), - MISSING_INPUT_FILE_ERROR - ) - } - if (!file.exists(args$compounds)) { - stop_with_status( - sprintf( - "Compounds file %s does not exist or cannot be accessed.", - args$compounds - ), - MISSING_INPUT_FILE_ERROR - ) - } - if (in_galaxy_env()) { - check_galaxy_args_validity(args) - } -} - -in_galaxy_env <- function() { - sysvars <- Sys.getenv() - sysvarnames <- names(sysvars) - return( - "_GALAXY_JOB_HOME_DIR" %in% sysvarnames - || "_GALAXY_JOB_TMP_DIR" %in% sysvarnames - || "GALAXY_MEMORY_MB" %in% sysvarnames - || "GALAXY_MEMORY_MB_PER_SLOT" %in% sysvarnames - || "GALAXY_SLOTS" %in% sysvarnames - ) -} - -check_galaxy_args_validity <- function(args) { - if (!file.exists(args$output)) { - stop_with_status( - sprintf( - "Output file %s does not exist or cannot be accessed.", - args$output - ), - MISSING_INPUT_FILE_ERROR - ) - } -} - -get_csv_or_tsv <- function( - path, - sep_stack = c("\t", ",", ";"), - sep_names = c("tab", "comma", "semicolon"), - header = TRUE, - quote = "\"" -) { - sep <- determine_csv_or_tsv_sep( - path = path, - sep_stack = sep_stack, - header = header, - quote = quote - ) - verbose_catf( - "%s separator has been determined for %s.\n", - sep_names[sep_stack == sep], - path - ) - return(read.table( - file = path, - sep = sep, - header = header, - quote = quote - )) -} - -determine_csv_or_tsv_sep <- function( - path, - sep_stack = c("\t", ",", ";"), - header = TRUE, - quote = "\"" -) { - count <- -1 - best_sep <- sep_stack[1] - for (sep in sep_stack) { - tryCatch({ - table <- read.table( - file = path, - sep = sep, - header = header, - quote = quote, - nrows = 1 - ) - if (ncol(table) > count) { - count <- ncol(table) - best_sep <- sep - } - }) - } - return(best_sep) -} - -uniformize_columns <- function(df) { - cols <- colnames(df) - for (func in c(tolower)) { - cols <- func(cols) - } - colnames(df) <- cols - return(df) -} - -handle_galaxy_param <- function(args) { - for (param in names(args)) { - if (is.character(args[[param]])) { - args[[param]] <- gsub("__ob__", "[", args[[param]]) - args[[param]] <- gsub("__cb__", "]", args[[param]]) - } - } - return(args) -} - -zip_pdfs <- function(processing_parameters) { - if (processing_parameters$do_pdf) { - if (zip <- Sys.getenv("R_ZIPCMD", "zip") == "") { - catf("R could not fin the zip executable. Trying luck: zip = \"zip\"") - zip <- "zip" - } else { - catf("Found zip executable at %s .", zip) - } - utils::zip( - processing_parameters$pdf_zip_path, - processing_parameters$pdf_path, - zip = zip - ) - } -} - -main <- function(args) { - if (args$version) { - catf("%s\n", MS2SNOOP_VERSION) - base::quit(status = 0) - } - if (in_galaxy_env()) { - print(sessionInfo()) - cat("\n\n") - } - check_args_validity(args) - args <- handle_galaxy_param(args) - if (args$ionization == "None") { - args$ionization <- NULL - } - if (args$debug) { - set_debug() - } - if (args$verbose) { - set_verbose() - } - precursors <- get_csv_or_tsv(args$precursors) - fragments <- get_csv_or_tsv(args$fragments) - compounds <- get_csv_or_tsv(args$compounds) - - compounds <- uniformize_columns(compounds) - mandatory_columns <- c( - "compound_name", - "mz", - "rtsec", - "inchikey" - ) - presents <- mandatory_columns %in% colnames(compounds) - if (!all(presents)) { - stop_with_status( - sprintf( - "Some columns are missing: %s", - paste(mandatory_columns[which(!presents)], collapse = ", ") - ), - BAD_PARAMETER_VALUE_ERROR - ) - } - - res_all <- data.frame() - processing_parameters <- list( - min_number_scan = args$min_number_scan, - mzdecimal = args$mzdecimal, - r_threshold = args$r_threshold, - seuil_ra = args$seuil_ra, - tolmz = args$tolmz, - tolrt = args$tolrt, - ionization = args$ionization, - do_pdf = nchar(args$pdf_path) > 0, - pdf_zip_path = args$pdf_path, - pdf_path = tempdir(), - fragment_match_delta = args$fragment_match_delta, - fragment_match_delta_unit = args$fragment_match_delta_unit - ) - for (i in seq_len(nrow(compounds))) { - processing_parameters$mzref <- compounds[["mz"]][i] - processing_parameters$rtref <- compounds[["rtsec"]][i] - processing_parameters$c_name <- compounds[["compound_name"]][i] - processing_parameters$inchikey <- compounds[["inchikey"]][i] - processing_parameters$elemcomposition <- compounds[["elemcomposition"]][i] - res_cor <- extract_fragments( - precursors = precursors, - fragments = fragments, - processing_parameters = processing_parameters - ) - if (!is.null(res_cor)) { - res_all <- rbind(res_all, res_cor) - } - } - - if (nrow(res_all) == 0) { - stop_with_status("No result at all!", NO_ANY_RESULT_ERROR) - } - - write.table( - x = res_all, - file = args$output, - sep = "\t", - row.names = FALSE - ) - zip_pdfs(processing_parameters) - unlink(processing_parameters$pdf_path, recursive = TRUE) -} - -global_debug <- FALSE -global_verbose <- FALSE -args <- optparse::parse_args(create_parser()) -main(args) - -warnings() +#' read and process mspurity W4M files +#' create a summary of fragment for each precursor and a graphics of peseudo +#' spectra + correlation on which checking of fragment is based on +#' V3 try to identify and process multiple files for 1 precursor which may +#' occur if different collision energy are used +#' V4 elimination of correlation = NA. Correlation is done with precursor, if +#' precursor is not present correlation with most intense peak +#' author: Jean-Francois Martin +#' V5 is versionned, lintR-compliant, packaged, unit-tested, documented and +#' tested against data from other labs. +#' new maintainer: Lain Pavot - lain.pavot@inrae.fr +#' +#' @import optparse +#' + + +get_version <- function() { + cmd <- commandArgs(trailingOnly = FALSE) + root <- dirname(gsub("--file=", "", cmd[grep("--file=", cmd)])) + readme <- readLines(file.path(root, "README.md")) + version_line <- readme[grepl(" * **@version**: ", readme, fixed = TRUE)] + return(gsub(".*: ", "", version_line)) +} + +defaults <- list( + MS2SNOOP_VERSION = get_version(), + MISSING_PARAMETER_ERROR = 1, + BAD_PARAMETER_VALUE_ERROR = 2, + MISSING_INPUT_FILE_ERROR = 3, + NO_ANY_RESULT_ERROR = 255, + DEFAULT_PRECURSOR_PATH = NULL, + DEFAULT_FRAGMENTS_PATH = NULL, + DEFAULT_COMPOUNDS_PATH = NULL, + DEFAULT_OUTPUT_PATH = "compound_fragments_result.txt", + DEFAULT_TOLMZ = 0.01, + DEFAULT_TOLRT = 20, + DEFAULT_MZDECIMAL = 3, + DEFAULT_R_THRESHOLD = 0.85, + DEFAULT_MINNUMBERSCAN = 8, + DEFAULT_SEUIL_RA = 0.05, + DEFAULT_FRAGMENTS_MATCH_DELTA = 10, + DEFAULT_FRAGMENTS_MATCH_DELTA_UNIT = "ppm", + DEFAULT_PDF_PATH = "" +) +env <- globalenv() +for (default in names(defaults)) { + assign(default, defaults[[default]], envir = env) + lockBinding(default, env) +} + +######################################################################## + +get_formulas <- function( + mzref, + spectra, + processing_parameters, + background = !TRUE +) { + if (is.vector(mzref) && length(mzref) > 1) { + return(lapply( + mzref, + function(mz) { + return(get_formulas( + mzref = mz, + spectra = spectra, + processing_parameters = processing_parameters, + background = background + )) + } + )) + } + input <- sprintf( + "%s-%s.ms", + gsub("[[:space:]]", "_", processing_parameters$c_name), + mzref + ) + create_ms_file(input, mzref, spectra, processing_parameters) + output <- sprintf( + "out/%s-%s.out", + gsub("[[:space:]]", "_", processing_parameters$c_name), + mzref + ) + command <- sprintf( + paste( + "sirius", + "--noCite", + "--noSummaries", + "--loglevel=WARNING", + "-i='%s'", + "-o='%s'", + "tree", + ## loglevel is not working taken into account during + ## sirius startup, so we filter outputs... + "2>&1 | grep '^(WARNING|SEVERE)'" + ), + input, + output + ) + verbose_catf( + ">> Sirius is running %swith the command: %s\n", + if (background) "in the background " else "", + command + ) + system( + command, + wait = !background, + ignore.stdout = background, + ignore.stderr = background + ) + return(extract_sirius_results(output, spectra$mz, processing_parameters)) +} + +create_ms_file <- function( + path, + mzref, + spectra, + processing_parameters +) { + file_content <- paste( + sprintf(">compound %s", processing_parameters$c_name), + sprintf(">ionization %s", processing_parameters$ionization), + sprintf(">parentmass %s", mzref), + sprintf(">formula %s", processing_parameters$elemcomposition), + sep = "\n" + ) + displayed_file_content <- sprintf( + "%s\n>collision\n%s", + file_content, + paste( + sprintf( + "%s %s", + spectra[1:3, "mz"], + spectra[1:3, "intensities"] + ), + collapse = "\n" + ) + ) + if (nrow(spectra) > 3) { + displayed_file_content <- sprintf( + "%s\n[... %s more rows of mz and intensities ...]", + displayed_file_content, + nrow(spectra) - 3 + ) + } + catf( + ">> MS file created for %s with content:\n%s\n", + processing_parameters$c_name, + displayed_file_content + ) + file_content <- sprintf( + "%s\n\n>collision\n%s", + file_content, + paste( + paste(spectra$mz, spectra$intensities), + collapse = "\n" + ) + ) + cat(file_content, file = path, append = FALSE) +} + +extract_sirius_results <- function( + output, + mz_list, + processing_parameters +) { + + delta <- processing_parameters$fragment_match_delta + delta_unit <- tolower(processing_parameters$fragment_match_delta_unit) + + output <- list.dirs(output, recursive = FALSE)[[1]] + + spectra_out_dir <- sprintf("%s/spectra", output) + spectra_filename <- sprintf( + "%s/%s", + spectra_out_dir, + list.files(spectra_out_dir)[[1]] + ) + + trees_out_dir <- sprintf("%s/trees", output) + trees_filename <- sprintf( + "%s/%s", + trees_out_dir, + list.files(trees_out_dir)[[1]] + ) + + if (!is.null(spectra_filename)) { + sirius_results <- get_csv_or_tsv(spectra_filename) + } else { + return(rep(NA, length(mz_list))) + } + if (!is.null(trees_filename)) { + sirius_results <- cbind(sirius_results, extract_sirius_ppm(trees_filename)) + } else { + return(rep(NA, length(mz_list))) + } + + fragment_matchings <- data.frame( + formula = NA, + ppm = NA, + mz = mz_list, + error = NA + ) + + sirius_results <- filter_sirius_with_delta( + sirius_results = sirius_results, + original_mz = fragment_matchings$mz, + delta = delta, + delta_unit = delta_unit + ) + + for (index in seq_len(nrow(sirius_results))) { + result <- sirius_results[index, ] + filter <- which(order(abs(fragment_matchings$mz - result$mz)) == 1) + fragment_matchings[filter, "formula"] <- result$formula + fragment_matchings[filter, "ppm"] <- result$ppm + catf( + "[OK] Fragment with m/z=%s matches %s with a difference of %s ppm\n", + fragment_matchings[filter, "mz"], result$formula, result$ppm + ) + } + return(fragment_matchings) +} + +filter_sirius_with_delta <- function( + sirius_results, + original_mz, + delta, + delta_unit +) { + if (is.numeric(delta) && !is.na(delta) && delta > 0) { + if (delta_unit == "ppm") { + filter <- abs(sirius_results$ppm) <= delta + fine <- which(filter) + not_fine <- which(!filter) + catf( + paste( + "[KO] fragment %s (m/z=%s) eleminated because ppm=%s is greater", + "than delta=%s\n" + ), + sirius_results[not_fine, ]$formula, + sirius_results[not_fine, ]$mz, + sirius_results[not_fine, ]$ppm, + delta + ) + sirius_results <- sirius_results[fine, ] + } else if (delta_unit == "mz") { + differences <- sapply( + sirius_results$mz, + function(mz) min(abs(original_mz - mz)) + ) + fine <- which(sapply( + sirius_results$mz, + function(mz) any(abs(original_mz - mz) <= delta) + )) + not_fine <- which(sapply( + sirius_results$mz, + function(mz) all(abs(original_mz - mz) > delta) + )) + catf( + paste( + "[KO] fragment %s eleminated because mz difference=%s is", + "greater than delta=%s\n" + ), + sirius_results[not_fine, ]$formula, + differences[not_fine], + delta + ) + sirius_results <- sirius_results[fine, ] + } + } + return(sirius_results) +} + +extract_sirius_ppm <- function(path) { + json <- file(path, "r") + suppressWarnings(json_lines <- readLines(json)) + close(json) + json_lines <- json_lines[ + grepl("\\s+\"(massDeviation|recalibratedMass)\" :", json_lines) + ] + json_lines <- gsub("^\\s+\"[^\"]+\" : \"?", "", json_lines) + ppms <- json_lines[seq(1, length(json_lines), 2)] + mz <- json_lines[seq(2, length(json_lines), 2)] + ppms <- as.numeric(gsub(" ppm .*", "", ppms)) + mz <- as.numeric(gsub(",$", "", mz)) + ordered <- order(mz) + return(list(ppm = ppms[ordered], recalibrated_mz = mz[ordered])) +} + +#' @title plot_pseudo_spectra +#' @param x +#' @param fid +#' @param sum_int +#' @param vmz +#' @param cor_abs_int +#' @param refcol +#' @param c_name +#' @description plot_pseudo_spectra +#' function to compute sum of intensities among scans for all +#' m/z kept (cor > r_threshold & minimum number of scans) +#' and plot pseudo spectra +#' x dataframe scan X fragments with scans number in the 1st column and +#' ions in next with intensities +#' fid file id when several a precursor has been detected in several files +plot_pseudo_spectra <- function( + x, + fid, + sum_int, + vmz, + cor_abs_int, + refcol, + meaned_mz, + processing_parameters +) { + ## du fait de la difference de nombre de colonne entre la dataframe qui + ## inclue les scans en 1ere col, mzRef se decale de 1 + refcol <- refcol - 1 + ## compute relative intensities max=100% + rel_int <- sum_int[-1] + rel_int <- rel_int / max(rel_int) + + if (processing_parameters$do_pdf) { + ## define max value on vertical axis (need to increase in order to plot the + ## label of fragments) + ymax <- max(rel_int) + 0.2 * max(rel_int) + + par(mfrow = c(2, 1)) + plot(vmz, rel_int, type = "h", ylim = c(0, ymax), + main = processing_parameters$c_name + ) + ## low correl coef. will be display in grey + cor_low <- which(round(cor_abs_int, 2) < processing_parameters$r_threshold) + + lbmzcor <- sprintf("%s(r=%s)", vmz, round(cor_abs_int, 2)) + + if (length(cor_low) > 0) { + text( + vmz[cor_low], + rel_int[cor_low], + lbmzcor[cor_low], + cex = 0.5, + col = "grey", + srt = 90, + adj = 0 + ) + if (length(vmz) - length(cor_low) > 1) { + text( + vmz[-c(refcol, cor_low)], + rel_int[-c(refcol, cor_low)], + lbmzcor[-c(refcol, cor_low)], + cex = 0.6, + col = 1, + srt = 90, + adj = 0 + ) + } + } else { + if (length(vmz) > 1) { + text( + vmz[-c(refcol)], + rel_int[-c(refcol)], + lbmzcor[-c(refcol)], + cex = 0.6, + col = 1, + srt = 90, + adj = 0 + ) + } + } + + text( + vmz[refcol], + rel_int[refcol], + lbmzcor[refcol], + cex = 0.8, + col = 2, + srt = 90, + adj = 0 + ) + } + + ## prepare result file + cor_valid <- (round(cor_abs_int, 2) >= processing_parameters$r_threshold) + + do_sirius <- TRUE + verbose_catf("Checking sirius parameters...\n") + if (is.null(processing_parameters$ionization)) { + do_sirius <- FALSE + verbose_catf("[KO] No ionization passed in parameter.\n") + } else { + verbose_catf("[OK] Ionization=%s.\n", processing_parameters$ionization) + } + if (is.na(processing_parameters$elemcomposition)) { + do_sirius <- FALSE + verbose_catf("[KO] Elemental composition is NA.\n") + } else if (length(processing_parameters$elemcomposition) < 1) { + do_sirius <- FALSE + verbose_catf("[KO] No elemental composition is provided.\n") + } else if (processing_parameters$elemcomposition == "") { + do_sirius <- FALSE + verbose_catf("[KO] Elemental composition is an empty string.\n") + } else { + verbose_catf( + "[OK] Elemental composition=%s.\n", + processing_parameters$elemcomposition + ) + } + + cp_res_length <- length(vmz) + ppm <- rep(NA, cp_res_length) + formulas <- rep(NA, cp_res_length) + if (do_sirius) { + verbose_catf("Everything is ok, preparing for sirius.\n") + formulas <- get_formulas( + mzref = processing_parameters$mzref, + spectra = data.frame(mz = meaned_mz, intensities = sum_int[-1]), + processing_parameters = processing_parameters + ) + if (nrow(formulas) == 0) { + catf("No formula found.\n") + } else { + ppm <- formulas$ppm + formulas <- formulas$formula + catf( + "Found %s formula for %s fragments\n", + length(formulas[which(!(is.na(formulas)))]), + cp_res_length + ) + } + } else { + verbose_catf("Sirius cannot be run.\n") + } + cp_res <- data.frame( + rep(processing_parameters$c_name, cp_res_length), + rep(processing_parameters$inchikey, cp_res_length), + rep(processing_parameters$elemcomposition, cp_res_length), + formulas, + meaned_mz, + ppm, + rep(fid, cp_res_length), + cor_abs_int, + sum_int[-1], + rel_int, + cor_valid + ) + + colnames(cp_res) <- c( + "compoundName", + "inchikey", + "elemcomposition", + "fragment", + "fragment_mz", + "ppm", + "fileid", + "CorWithPrecursor", + "AbsoluteIntensity", + "relativeIntensity", + "corValid" + ) + return(cp_res) +} + +#' +#' @title extract_fragments +#' +#' @param precursors the precursor list from mspurity +#' @param fragments the fragments list from ms purity +# ' @param mzref +# ' @param rtref +# ' @param c_name +# ' @param inchikey +# ' @param elemcomposition +#' @param processing_parameters +#' @returns +#' +#' @description +#' function for extraction of fragments corresponding to precursors +#' detected by MSPurity +extract_fragments <- function( ## nolint cyclocomp_linter + precursors, + fragments, + processing_parameters +) { + ## filter precursor in the precursors file based on mz and rt in the + ## compound list + catf("processing %s\n", processing_parameters$c_name) + verbose_catf("===\n") + param <- processing_parameters + selected_precursors <- which( + (abs(precursors$precurMtchMZ - param$mzref) <= param$tolmz) + & (abs(precursors$precurMtchRT - param$rtref) <= param$tolrt) + ) + rm(param) + + verbose_catf( + "> %s precursors selected with mz=%s±%s and rt=%s±%s\n", + length(selected_precursors), + processing_parameters$mzref, + processing_parameters$tolmz, + processing_parameters$rtref, + processing_parameters$tolrt + ) + + ## check if there is the precursor in the file + + if (length(selected_precursors) < 1) { + cat("> non detected in precursor file\n") + show_end_processing() + return(NULL) + } + + precursors <- precursors[selected_precursors, ] + + ## check if fragments corresponding to precursor are found in several + ## files (collision energy) + ## this lead to a processing for each fileid + file_ids <- as.character(sort(unique(precursors$fileid))) + if (length(file_ids) > 1) { + catf("> several files detected for this compounds :\n") + } else if (length(file_ids) < 1 || nrow(precursors) < 1) { + return(data.frame()) + } + + res_comp <- data.frame() + for (curent_file_id in file_ids) { + curent_precursors <- precursors[precursors$fileid == curent_file_id, ] + selected_fragments <- fragments[ + fragments$grpid %in% as.character(curent_precursors$grpid) + & fragments$fileid == curent_file_id, + ] + filtered_fragments <- selected_fragments[ + selected_fragments$ra > processing_parameters$seuil_ra, + ] + if (nrow(filtered_fragments) != 0) { + res_comp_by_file <- process_file( + curent_file_id = curent_file_id, + precursor_mz = curent_precursors$mz, + filtered_fragments = filtered_fragments, + processing_parameters = processing_parameters + ) + if (!is.null(res_comp_by_file)) { + res_comp <- rbind(res_comp, res_comp_by_file) + } + } else { + catf("No fragment found for in fragment file\n") + } + } + return(unique(res_comp)) +} + +process_file <- function( + curent_file_id, + precursor_mz, + filtered_fragments, + processing_parameters +) { + mznominal <- round(x = filtered_fragments$mz, digits = 0) + meaned_mz <- round( + aggregate( + data.frame( + mz = filtered_fragments$mz, + mznominal = mznominal + ), + list(mznominal), + FUN = mean + )$mz, + digits = processing_parameters$mzdecimal + ) + filtered_fragments <- data.frame(filtered_fragments, mznominal) + + ## creation of cross table row=scan col=mz X=ra + + vmz <- as.character(sort(unique(filtered_fragments$mznominal))) + + ds_abs_int <- create_ds_abs_int(vmz, filtered_fragments) + + if (global_debug) { + print(ds_abs_int) + } + + ## elimination of mz with less than min_number_scan scans (user defined + ## parameter) + xmz <- rep(NA, ncol(ds_abs_int) - 1) + sum_int <- rep(NA, ncol(ds_abs_int)) + nbxmz <- 0 + nb_scan_check <- min(nrow(ds_abs_int), processing_parameters$min_number_scan) + + for (j in 2:ncol(ds_abs_int)) { + sum_int[j] <- sum(ds_abs_int[j], na.rm = TRUE) + if (sum(!is.na(ds_abs_int[[j]])) < nb_scan_check) { + nbxmz <- nbxmz + 1 + xmz[nbxmz] <- j + } + } + + xmz <- xmz[-which(is.na(xmz))] + if (length(xmz) > 0) { + ds_abs_int <- ds_abs_int[, -c(xmz)] + sum_int <- sum_int[-c(xmz)] + ## liste des mz keeped decale de 1 avec ds_abs_int + vmz <- as.numeric(vmz[-c(xmz - 1)]) + meaned_mz <- meaned_mz[-c(xmz - 1)] + } + + ## mz of precursor in data precursor to check correlation with + mz_prec <- paste0( + "mz", + round(mean(precursor_mz), processing_parameters$mzdecimal) + ) + ## reference ion for correlation computing = precursor OR maximum + ## intensity ion in precursor is not present + refcol <- which(colnames(ds_abs_int) == mz_prec) + if (length(refcol) == 0) { + refcol <- which(sum_int == max(sum_int, na.rm = TRUE)) + } + + if (processing_parameters$do_pdf) { + start_pdf(processing_parameters, curent_file_id) + } + + ## Pearson correlations between absolute intensities computing + cor_abs_int <- rep(NA, length(vmz)) + + if (length(refcol) > 0) { + for (i in 2:length(ds_abs_int)) { + cor_abs_int[i - 1] <- stats::cor( + x = ds_abs_int[[refcol]], + y = ds_abs_int[[i]], + use = "pairwise.complete.obs", + method = "pearson" + ) + debug_catf( + "Correlation between %s and %s: %s\n", + paste(ds_abs_int[[refcol]], collapse = ";"), + paste(ds_abs_int[[i]], collapse = ";"), + paste(cor_abs_int[i - 1], collapse = ";") + ) + if (processing_parameters$do_pdf) { + pdf_plot_ds_abs_int( + processing_parameters$c_name, + ds_abs_int, + refcol, + i, + round(cor_abs_int[i - 1], 2) + ) + } + } + ## plot pseudo spectra + res_comp_by_file <- plot_pseudo_spectra( + x = ds_abs_int, + fid = curent_file_id, + sum_int = sum_int, + vmz = vmz, + cor_abs_int = cor_abs_int, + refcol = refcol, + meaned_mz = meaned_mz, + processing_parameters = processing_parameters + ) + catf( + "%s has been processed and %s fragments have been found.\n", + processing_parameters$c_name, + nrow(res_comp_by_file) + ) + } else { + res_comp_by_file <- NULL + cat(">> non detected in fragments file \n") + } + show_end_processing() + if (processing_parameters$do_pdf) { + end_pdf() + } + return(res_comp_by_file) +} + +create_ds_abs_int <- function(vmz, filtered_fragments) { + verbose_catf( + ">> fragments: %s\n", + paste(vmz, collapse = " ") + ) + ds_abs_int <- create_int_mz(vmz[1], filtered_fragments) + for (mz in vmz[-1]) { + int_mz <- create_int_mz(mz, filtered_fragments) + ds_abs_int <- merge( + x = ds_abs_int, + y = int_mz, + by.x = 1, + by.y = 1, + all.x = TRUE, + all.y = TRUE + ) + } + return(ds_abs_int) +} + +create_int_mz <- function(mz, filtered_fragments) { + ## absolute intensity + int_mz <- filtered_fragments[ + filtered_fragments$mznominal == mz, + c("acquisitionNum", "i") + ] + colnames(int_mz)[2] <- paste0("mz", mz) + ## average intensities of mass in duplicate scans + comp_scans <- aggregate(x = int_mz, by = list(int_mz[[1]]), FUN = mean) + return(comp_scans[, -1]) +} + +show_end_processing <- function() { + verbose_catf("==========\n") + cat("\n") +} + +start_pdf <- function(processing_parameters, curent_file_id) { + if (!dir.exists(processing_parameters$pdf_path)) { + dir.create(processing_parameters$pdf_path, recursive = TRUE) + } + pdf( + file = sprintf( + "%s/%s_processing_file%s.pdf", + processing_parameters$pdf_path, + processing_parameters$c_name, + curent_file_id + ), + width = 8, + height = 11 + ) + par(mfrow = c(3, 2)) +} + +pdf_plot_ds_abs_int <- function(c_name, ds_abs_int, refcol, i, r_coef) { + plot( + ds_abs_int[[refcol]], + ds_abs_int[[i]], + xlab = colnames(ds_abs_int)[refcol], + ylab = colnames(ds_abs_int)[i], + main = sprintf( + "%s corr coeff r=%s", c_name, r_coef + ) + ) +} +end_pdf <- function() { + dev.off() +} + +set_global <- function(var, value) { + assign(var, value, envir = globalenv()) +} + +set_debug <- function() { + set_global("global_debug", TRUE) +} + +unset_debug <- function() { + set_global("global_debug", FALSE) +} + +set_verbose <- function() { + set_global("global_verbose", TRUE) +} + +unset_verbose <- function() { + set_global("global_verbose", FALSE) +} + +verbose_catf <- function(...) { + if (global_verbose) { + cat(sprintf(...), sep = "") + } +} + + +debug_catf <- function(...) { + if (global_debug) { + cat(sprintf(...), sep = "") + } +} + +catf <- function(...) { + cat(sprintf(...), sep = "") +} + +create_parser <- function() { + parser <- optparse::OptionParser() + parser <- optparse::add_option( + parser, + c("-v", "--verbose"), + action = "store_true", + default = FALSE, + help = paste( + "[default %default]", + "Print extra output" + ) + ) + parser <- optparse::add_option( + parser, + c("-V", "--version"), + action = "store_true", + default = FALSE, + help = "Prints version and exits" + ) + parser <- optparse::add_option( + parser, + c("-d", "--debug"), + action = "store_true", + default = FALSE, + help = paste( + "[default %default]", + "Print debug outputs" + ) + ) + parser <- optparse::add_option( + parser, + c("-o", "--output"), + type = "character", + default = DEFAULT_OUTPUT_PATH, + action = "store", + help = "Path to the output file [default %default]" + ) + parser <- optparse::add_option( + parser, + c("-p", "--precursors"), + type = "character", + default = DEFAULT_PRECURSOR_PATH, + action = "store", + help = "Path to the precursors file [default %default]" + ) + parser <- optparse::add_option( + parser, + c("-f", "--fragments"), + type = "character", + default = DEFAULT_FRAGMENTS_PATH, + action = "store", + help = "Path to the fragments file [default %default]" + ) + parser <- optparse::add_option( + parser, + c("-c", "--compounds"), + type = "character", + default = DEFAULT_COMPOUNDS_PATH, + action = "store", + help = "Path to the compounds file [default %default]" + ) + parser <- optparse::add_option( + parser, + c("--tolmz"), + type = "numeric", + action = "store", + default = DEFAULT_TOLMZ, + metavar = "number", + help = paste( + "[default %default]", + "Tolerance for MZ (in Dalton) to match the standard in the compounds" + ) + ) + parser <- optparse::add_option( + parser, + c("--tolrt"), + type = "integer", + action = "store", + default = DEFAULT_TOLRT, + metavar = "number", + help = paste( + "[default %default]", + "RT (in seconds) to match the standard in the compounds" + ) + ) + parser <- optparse::add_option( + parser, + c("--seuil_ra"), + type = "numeric", + action = "store", + default = DEFAULT_SEUIL_RA, + metavar = "number", + help = paste( + "[default %default]", + "relative intensity threshold" + ), + ) + parser <- optparse::add_option( + parser, + c("--mzdecimal"), + type = "integer", + default = DEFAULT_MZDECIMAL, + action = "store", + help = paste( + "[default %default]", + "Number of decimal to write for MZ" + ), + metavar = "number" + ) + parser <- optparse::add_option( + parser, + c("--r_threshold"), + type = "integer", + default = DEFAULT_R_THRESHOLD, + action = "store", + help = paste( + "[default %default]", + "R-Pearson correlation threshold between precursor and fragment", + "absolute intensity" + ), + metavar = "number" + ) + parser <- optparse::add_option( + parser, + c("--min_number_scan"), + type = "numeric", + action = "store", + default = DEFAULT_MINNUMBERSCAN, + help = paste( + "[default %default]", + "Fragments are kept if there are found in a minimum number", + "of min_number_scan scans" + ), + metavar = "number" + ) + parser <- optparse::add_option( + parser, + c("--pdf_path"), + type = "character", + default = DEFAULT_PDF_PATH, + help = paste( + "[default %default]", + "PDF files output path" + ) + ) + parser <- optparse::add_option( + parser, + c("--ionization"), + type = "character", + action = "store", + default = "None", + help = paste( + "[default %default]", + "Which ionization to use for sirius" + ), + metavar = "character" + ) + parser <- optparse::add_option( + parser, + c("--fragment_match_delta"), + type = "numeric", + action = "store", + default = DEFAULT_FRAGMENTS_MATCH_DELTA, + help = paste( + "[default %default]", + "Fragment match delta" + ), + metavar = "numeric" + ) + parser <- optparse::add_option( + parser, + c("--fragment_match_delta_unit"), + type = "character", + action = "store", + default = DEFAULT_FRAGMENTS_MATCH_DELTA_UNIT, + help = paste( + "[default %default]", + "Fragment match delta" + ), + metavar = "character" + ) + return(parser) +} + +stop_with_status <- function(msg, status) { + sink(stderr()) + message(sprintf("Error: %s", msg)) + message(sprintf("Error code: %s", status)) + sink(NULL) + base::quit(status = status) +} + +check_args_validity <- function(args) { ## nolint cyclocomp_linter + if (length(args$output) == 0 || nchar(args$output[1]) == 0) { + stop_with_status( + "Missing output parameters. Please set it with --output.", + MISSING_PARAMETER_ERROR + ) + } + if (length(args$precursors) == 0 || nchar(args$precursors[1]) == 0) { + stop_with_status( + "Missing precursors parameters. Please set it with --precursors.", + MISSING_PARAMETER_ERROR + ) + } + if (length(args$fragments) == 0 || nchar(args$fragments[1]) == 0) { + stop_with_status( + "Missing fragments parameters. Please set it with --fragments.", + MISSING_PARAMETER_ERROR + ) + } + if (length(args$compounds) == 0 || nchar(args$compounds[1]) == 0) { + stop_with_status( + "Missing compounds parameters. Please set it with --compounds.", + MISSING_PARAMETER_ERROR + ) + } + if (!file.exists(args$precursors)) { + stop_with_status( + sprintf( + "Precursors file %s does not exist or cannot be accessed.", + args$precursors + ), + MISSING_INPUT_FILE_ERROR + ) + } + if (!file.exists(args$fragments)) { + stop_with_status( + sprintf( + "Fragments file %s does not exist or cannot be accessed.", + args$fragments + ), + MISSING_INPUT_FILE_ERROR + ) + } + if (!file.exists(args$compounds)) { + stop_with_status( + sprintf( + "Compounds file %s does not exist or cannot be accessed.", + args$compounds + ), + MISSING_INPUT_FILE_ERROR + ) + } + if (in_galaxy_env()) { + check_galaxy_args_validity(args) + } +} + +in_galaxy_env <- function() { + sysvars <- Sys.getenv() + sysvarnames <- names(sysvars) + return( + "_GALAXY_JOB_HOME_DIR" %in% sysvarnames + || "_GALAXY_JOB_TMP_DIR" %in% sysvarnames + || "GALAXY_MEMORY_MB" %in% sysvarnames + || "GALAXY_MEMORY_MB_PER_SLOT" %in% sysvarnames + || "GALAXY_SLOTS" %in% sysvarnames + ) +} + +check_galaxy_args_validity <- function(args) { + if (!file.exists(args$output)) { + stop_with_status( + sprintf( + "Output file %s does not exist or cannot be accessed.", + args$output + ), + MISSING_INPUT_FILE_ERROR + ) + } +} + +get_csv_or_tsv <- function( + path, + sep_stack = c("\t", ",", ";"), + sep_names = c("tab", "comma", "semicolon"), + header = TRUE, + quote = "\"" +) { + sep <- determine_csv_or_tsv_sep( + path = path, + sep_stack = sep_stack, + header = header, + quote = quote + ) + verbose_catf( + "%s separator has been determined for %s.\n", + sep_names[sep_stack == sep], + path + ) + return(read.table( + file = path, + sep = sep, + header = header, + quote = quote + )) +} + +determine_csv_or_tsv_sep <- function( + path, + sep_stack = c("\t", ",", ";"), + header = TRUE, + quote = "\"" +) { + count <- -1 + best_sep <- sep_stack[1] + for (sep in sep_stack) { + tryCatch({ + table <- read.table( + file = path, + sep = sep, + header = header, + quote = quote, + nrows = 1 + ) + if (ncol(table) > count) { + count <- ncol(table) + best_sep <- sep + } + }) + } + return(best_sep) +} + +uniformize_columns <- function(df) { + cols <- colnames(df) + for (func in c(tolower)) { + cols <- func(cols) + } + colnames(df) <- cols + return(df) +} + +handle_galaxy_param <- function(args) { + for (param in names(args)) { + if (is.character(args[[param]])) { + args[[param]] <- gsub("__ob__", "[", args[[param]]) + args[[param]] <- gsub("__cb__", "]", args[[param]]) + } + } + return(args) +} + +zip_pdfs <- function(processing_parameters) { + if (processing_parameters$do_pdf) { + if (zip <- Sys.getenv("R_ZIPCMD", "zip") == "") { + catf("R could not fin the zip executable. Trying luck: zip = \"zip\"") + zip <- "zip" + } else { + catf("Found zip executable at %s .", zip) + } + utils::zip( + processing_parameters$pdf_zip_path, + processing_parameters$pdf_path, + zip = zip + ) + } +} + +main <- function(args) { + if (args$version) { + catf("%s\n", MS2SNOOP_VERSION) + base::quit(status = 0) + } + if (in_galaxy_env()) { + print(sessionInfo()) + cat("\n\n") + } + check_args_validity(args) + args <- handle_galaxy_param(args) + if (args$ionization == "None") { + args$ionization <- NULL + } + if (args$debug) { + set_debug() + } + if (args$verbose) { + set_verbose() + } + precursors <- get_csv_or_tsv(args$precursors) + fragments <- get_csv_or_tsv(args$fragments) + compounds <- get_csv_or_tsv(args$compounds) + + compounds <- uniformize_columns(compounds) + mandatory_columns <- c( + "compound_name", + "mz", + "rtsec", + "inchikey" + ) + presents <- mandatory_columns %in% colnames(compounds) + if (!all(presents)) { + stop_with_status( + sprintf( + "Some columns are missing: %s", + paste(mandatory_columns[which(!presents)], collapse = ", ") + ), + BAD_PARAMETER_VALUE_ERROR + ) + } + + res_all <- data.frame() + processing_parameters <- list( + min_number_scan = args$min_number_scan, + mzdecimal = args$mzdecimal, + r_threshold = args$r_threshold, + seuil_ra = args$seuil_ra, + tolmz = args$tolmz, + tolrt = args$tolrt, + ionization = args$ionization, + do_pdf = nchar(args$pdf_path) > 0, + pdf_zip_path = args$pdf_path, + pdf_path = tempdir(), + fragment_match_delta = args$fragment_match_delta, + fragment_match_delta_unit = args$fragment_match_delta_unit + ) + for (i in seq_len(nrow(compounds))) { + processing_parameters$mzref <- compounds[["mz"]][i] + processing_parameters$rtref <- compounds[["rtsec"]][i] + processing_parameters$c_name <- compounds[["compound_name"]][i] + processing_parameters$inchikey <- compounds[["inchikey"]][i] + processing_parameters$elemcomposition <- compounds[["elemcomposition"]][i] + res_cor <- extract_fragments( + precursors = precursors, + fragments = fragments, + processing_parameters = processing_parameters + ) + if (!is.null(res_cor)) { + res_all <- rbind(res_all, res_cor) + } + } + + if (nrow(res_all) == 0) { + stop_with_status("No result at all!", NO_ANY_RESULT_ERROR) + } + + write.table( + x = res_all, + file = args$output, + sep = "\t", + row.names = FALSE + ) + zip_pdfs(processing_parameters) + unlink(processing_parameters$pdf_path, recursive = TRUE) +} + +global_debug <- FALSE +global_verbose <- FALSE +args <- optparse::parse_args(create_parser()) +main(args) + +warnings() diff -r 78d5a12406c2 -r 77abacd33c31 MS2snoop.xml --- a/MS2snoop.xml Fri Aug 05 17:25:45 2022 +0000 +++ b/MS2snoop.xml Fri Sep 30 16:18:56 2022 +0000 @@ -1,9 +1,4 @@ - + MS1/MS2 spectra and associated adducts extraction and cleaning @@ -33,11 +28,13 @@ - Rscript '$__tool_directory__/MS2snoop.R' --version | head -n 1 + - +]]> - - - - - - - - -
- @@ -166,12 +109,7 @@ - - @@ -193,71 +128,33 @@
- - -
- - + + advenced['pdf'] - - - - + + + + @@ -267,23 +164,11 @@ - - - + + + - + @@ -293,23 +178,11 @@ - - - + + + - + @@ -319,24 +192,12 @@ - - - + + + - + @@ -349,23 +210,11 @@ This test mixes tsv, csv, and so, and ms2snoop is expected handle them like usual. --> - - - + + + - + @@ -432,26 +281,17 @@ This test uses old format for molecules file. Is is expected to fail --> - - - + + + - + +]]> + diff -r 78d5a12406c2 -r 77abacd33c31 README.md --- a/README.md Fri Aug 05 17:25:45 2022 +0000 +++ b/README.md Fri Sep 30 16:18:56 2022 +0000 @@ -5,7 +5,7 @@ ----------- * **@name**: MS2 Snoop - * **@version**: 2.1.0 + * **@version**: 2.2.0 * **@authors**: Jean François Martin (INRAE), Kevin Wagner (INRAE) * **@maintainers**: Lain Pavot (PFEM - INRAE - MetaboHUB) * **@init date**: 2022, April diff -r 78d5a12406c2 -r 77abacd33c31 macros.xml --- a/macros.xml Fri Aug 05 17:25:45 2022 +0000 +++ b/macros.xml Fri Sep 30 16:18:56 2022 +0000 @@ -1,18 +1,18 @@ - + LC_ALL=C Rscript + + .. class:: infomark -**Authors** Jean-Francois Martin (jean-francois.martin@inrae.fr), Lain Pavot (lain.pavot@inrae.fr), Kevin Wagner (kevin.wagner@inrae.fr) +**Authors** Jean-Francois Martin (jean-francois.martin@inrae.fr), Kevin Wagner (kevin.wagner@inrae.fr), Lain Pavot (lain.pavot@inrae.fr) .. class:: infomark --------------------------------------------------- - - - - - + + - - - + + - - + + + +]]> + - 2.1.0 - 0 + 2.2.0 + 0 - - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - + + + + + - - - - + + + + - - - - - + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff -r 78d5a12406c2 -r 77abacd33c31 test-data/compound_fragments_result.txt --- a/test-data/compound_fragments_result.txt Fri Aug 05 17:25:45 2022 +0000 +++ b/test-data/compound_fragments_result.txt Fri Sep 30 16:18:56 2022 +0000 @@ -1,743 +1,743 @@ "compoundName" "inchikey" "elemcomposition" "fragment" "fragment_mz" "ppm" "fileid" "CorWithPrecursor" "AbsoluteIntensity" "relativeIntensity" "corValid" -"2-diethylamino-6-methyl pyrimidin-4-ol one" NA NA NA 84 NA "7" 0.601436519480403 406.383798606 0.00344160476662782 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" NA NA NA 123 NA "7" -0.167860259307508 295.871994004 0.00250569650751035 FALSE -"2-diethylamino-6-methyl pyrimidin-4-ol one" NA NA NA 126 NA "7" 0.907929868611774 430.137959956 0.00364277527394095 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" NA NA NA 137 NA "7" 0.676403388268515 430.806630151 0.00364843814371653 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" NA NA NA 146 NA "7" -0.125051837812104 538.358772757 0.00455928145962519 FALSE -"2-diethylamino-6-methyl pyrimidin-4-ol one" NA NA NA 148 NA "7" 0.1558553290912 143.310915941 0.00121367912083162 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" NA NA NA 149 NA "7" -0.276972713799663 617.416199707 0.00522880720932724 FALSE -"2-diethylamino-6-methyl pyrimidin-4-ol one" NA NA NA 150 NA "7" -0.410733329402461 5080.527405 0.0430262411887723 FALSE -"2-diethylamino-6-methyl pyrimidin-4-ol one" NA NA NA 151 NA "7" -0.243340932574313 218.539256565 0.00185077690023418 FALSE 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0.00248871682402531 FALSE -"Hydroxy-tebuconazole" NA NA NA 266 NA "3" 0.442854013871549 224.958957681 0.000527787287781417 TRUE -"Hydroxy-tebuconazole" NA NA NA 268 NA "3" 0.333877814717464 167.482578998 0.00039293912556858 TRUE -"Hydroxy-tebuconazole" NA NA NA 276 NA "3" 0.814390714374443 472.387895585 0.00110829250260451 TRUE -"Hydroxy-tebuconazole" NA NA NA 278 NA "3" 0.275231308762053 379.986748698 0.000891505621983662 TRUE -"Hydroxy-tebuconazole" NA NA NA 280 NA "3" 0.650641022624376 416.402436187 0.000976942259540319 TRUE -"Hydroxy-tebuconazole" NA NA NA 282 NA "3" 0.782140125615591 155.801819332 0.000365534320145864 TRUE -"Hydroxy-tebuconazole" NA NA NA 288 NA "3" 0.702501554923525 901.789572159 0.00211573292011017 TRUE -"Hydroxy-tebuconazole" NA NA NA 292 NA "3" -0.282700274468723 1574.001168335 0.00369284164615631 FALSE -"Hydroxy-tebuconazole" NA NA NA 296 NA "3" -0.00403563274731662 354.472442154 0.000831645251055126 TRUE -"Hydroxy-tebuconazole" NA NA NA 306 NA "3" 0.939487898745732 6832.34144213 0.0160296926875516 TRUE -"Hydroxy-tebuconazole" NA NA NA 307 NA "3" 0.647420935806109 170.978830823 0.000401141854133558 TRUE -"Hydroxy-tebuconazole" NA NA NA 324 NA "3" 1 426230.3448547 1 TRUE -"Hydroxy-tebuconazole" NA NA NA 325 NA "3" 0.526687588803207 740.769098256 0.0017379548575044 TRUE -"Isoproturon" NA NA NA 72 NA "2" 0.993086605464471 59907.1442268 0.115787147683237 TRUE -"Isoproturon" NA NA NA 120 NA "2" 0.927282017838371 790.062006494 0.00152701363761405 TRUE -"Isoproturon" NA NA NA 134 NA "2" 0.71269989274101 432.2311039 0.000835406315999436 TRUE -"Isoproturon" NA NA NA 137 NA "2" 0.213034502535958 770.65881154 0.00148951158959186 TRUE -"Isoproturon" NA NA NA 147 NA "2" -0.543816345969317 1151.6802063 0.00222594095999428 FALSE -"Isoproturon" NA NA NA 149 NA "2" 0.500520723996853 390.29506684 0.000754353310068573 TRUE -"Isoproturon" NA NA NA 161 NA "2" 0.400505614578046 614.84665681 0.00118836144792821 TRUE -"Isoproturon" NA NA NA 162 NA "2" 0.804730923860733 2048.22309885 0.00395875840011529 TRUE -"Isoproturon" NA NA NA 165 NA "2" 0.985177338187729 41795.7801207 0.0807819205510825 TRUE -"Isoproturon" NA NA NA 174 NA "2" -0.672244697055266 2538.22496785 0.00490582271945875 FALSE -"Isoproturon" NA NA NA 175 NA "2" -0.891117335203028 41310.6113296 0.0798441974933163 FALSE -"Isoproturon" NA NA NA 179 NA "2" 0.106337033555785 305.46005153 0.000590386147667693 TRUE -"Isoproturon" NA NA NA 189 NA "2" -0.557815616548336 2256.78026215 0.00436185287873026 FALSE -"Isoproturon" NA NA NA 193 NA "2" -0.457037805653279 900.73918538 0.00174092793819098 FALSE -"Isoproturon" NA NA NA 207 NA "2" 1 517390.275393 1 TRUE -"Malathion dicarboxilic acid" NA NA NA 99 NA "5" 0.0390122357382497 146.313006405 0.00728513388971739 TRUE -"Malathion dicarboxilic acid" NA NA NA 101 NA "5" -0.00307888841729598 435.762945656 0.0216972604232751 TRUE -"Malathion dicarboxilic acid" NA NA NA 105 NA "5" 0.592401757892981 89.451040273 0.00445389525494049 TRUE -"Malathion dicarboxilic acid" NA NA NA 111 NA "5" 0.238541386362055 129.625732421 0.00645425064690212 TRUE -"Malathion dicarboxilic acid" NA NA NA 113 NA "5" -0.181700362244182 214.697242755 0.0106900828412605 FALSE -"Malathion dicarboxilic acid" NA NA NA 115 NA "5" -0.231992590984375 169.733005041 0.00845124912412097 FALSE -"Malathion dicarboxilic acid" NA NA NA 125 NA "5" -0.250900317999769 976.859200016 0.0486392169662613 FALSE -"Malathion dicarboxilic acid" NA NA NA 127 NA "5" -0.120496404762161 251.457530026 0.0125204301300888 FALSE -"Malathion dicarboxilic acid" NA NA NA 133 NA "5" -0.00480587756063445 106.381536014 0.00529688885696561 TRUE -"Malathion dicarboxilic acid" NA NA NA 135 NA "5" -0.090209154235706 265.367501262 0.0132130274961485 FALSE -"Malathion dicarboxilic acid" NA NA NA 143 NA "5" -0.131857430656449 2027.15360119 0.100934877647263 FALSE -"Malathion dicarboxilic acid" NA NA NA 145 NA "5" -0.00327881805976476 340.208190446 0.0169394524702548 TRUE -"Malathion dicarboxilic acid" NA NA NA 155 NA "5" -0.103996527690727 89.39838505 0.00445127347606401 FALSE -"Malathion dicarboxilic acid" NA NA NA 157 NA "5" 0.0930278278084389 283.279369826 0.014104885054885 TRUE -"Malathion dicarboxilic acid" NA NA NA 159 NA "5" -0.0612368257690917 11570.4075283 0.576107142306516 FALSE -"Malathion dicarboxilic acid" NA NA NA 171 NA "5" -0.19710660695736 343.725625045 0.0171145905706306 FALSE -"Malathion dicarboxilic acid" NA NA NA 173 NA "5" 0.0378284550947032 276.705667733 0.0137775710239911 TRUE -"Malathion dicarboxilic acid" NA NA NA 174 NA "5" -0.540544488822746 145.849533325 0.00726205690206577 FALSE -"Malathion dicarboxilic acid" NA NA NA 175 NA "5" 0.184070758387235 1172.409335654 0.0583759379542223 TRUE -"Malathion dicarboxilic acid" NA NA NA 177 NA "5" -0.140789116062933 180.05658699 0.00896527503724966 FALSE -"Malathion dicarboxilic acid" NA NA NA 183 NA "5" -0.260101643573225 92.657263754 0.00461353770856342 FALSE -"Malathion dicarboxilic acid" NA NA NA 185 NA "5" 0.435155306012117 212.018755439 0.0105567171262197 TRUE -"Malathion dicarboxilic acid" NA NA NA 187 NA "5" -0.0466843753550633 941.066299451 0.0468570372453718 FALSE -"Malathion dicarboxilic acid" NA NA NA 189 NA "5" -0.395771460619492 146.580297463 0.00729844269385517 FALSE -"Malathion dicarboxilic acid" NA NA NA 190 NA "5" -0.103737669048405 148.989129555 0.0074183818895511 FALSE -"Malathion dicarboxilic acid" NA NA NA 193 NA "5" -0.153009009646862 1596.369196382 0.0794855058946147 FALSE -"Malathion dicarboxilic acid" NA NA NA 197 NA "5" -0.244011968974358 179.884572989 0.00895671021407378 FALSE -"Malathion dicarboxilic acid" NA NA NA 199 NA "5" 0.150914124088504 276.667024113 0.0137756469028716 TRUE -"Malathion dicarboxilic acid" NA NA NA 201 NA "5" -0.10556131251179 239.864170096 0.0119431801548682 FALSE -"Malathion dicarboxilic acid" NA NA NA 203 NA "5" -0.0442733202671276 1407.858670707 0.0700992971568763 FALSE -"Malathion dicarboxilic acid" NA NA NA 205 NA "5" -0.206299059029665 130.40357304 0.00649298044402344 FALSE -"Malathion dicarboxilic acid" NA NA NA 213 NA "5" 0.034041946036616 282.143243319 0.0140483156908721 TRUE -"Malathion dicarboxilic acid" NA NA NA 215 NA "5" -0.0174569064315414 4632.372268515 0.23065244185969 FALSE -"Malathion dicarboxilic acid" NA NA NA 216 NA "5" 0.11460473836849 152.968408575 0.00761651588431708 TRUE -"Malathion dicarboxilic acid" NA NA NA 217 NA "5" -0.0749466491463488 149.235903278 0.00743066910622917 FALSE -"Malathion dicarboxilic acid" NA NA NA 219 NA "5" -0.229702200918307 275.246332175 0.0137049086189782 FALSE -"Malathion dicarboxilic acid" NA NA NA 229 NA "5" -0.0736331507746074 508.844859597 0.0253361134621037 FALSE -"Malathion dicarboxilic acid" NA NA NA 231 NA "5" -0.398924747325029 548.515546309 0.027311373702427 FALSE -"Malathion dicarboxilic acid" NA NA NA 233 NA "5" -0.0593443075085707 5883.46527449 0.292946152316215 FALSE -"Malathion dicarboxilic acid" NA NA NA 239 NA "5" -0.250539714331339 289.00519777 0.0143899822190159 FALSE -"Malathion dicarboxilic acid" NA NA NA 243 NA "5" -0.0531886469417714 3332.41069708 0.165925495622409 FALSE -"Malathion dicarboxilic acid" NA NA NA 245 NA "5" -0.230543139716182 369.79291249 0.0184125181017819 FALSE -"Malathion dicarboxilic acid" NA NA NA 247 NA "5" -0.0791167715438849 453.035788533 0.0225572999789294 FALSE -"Malathion dicarboxilic acid" NA NA NA 257 NA "5" 0.106470337603423 20083.7772675 1 TRUE -"Malathion dicarboxilic acid" NA NA NA 261 NA "5" 0.355868386838636 138.486630433 0.00689544743443765 TRUE -"Malathion dicarboxilic acid" NA NA NA 275 NA "5" 1 7538.973325 0.375376266356017 TRUE -"Methamidophos" NA NA NA 94 NA "10" 0.976908842717177 9354.73397623 0.0482149771671354 TRUE -"Methamidophos" NA NA NA 100 NA "10" 0.513584871583348 164.780854231 0.000849292469942643 TRUE -"Methamidophos" NA NA NA 110 NA "10" 0.284212959905891 434.336410282 0.0022386013496283 TRUE -"Methamidophos" NA NA NA 112 NA "10" 0.703154152581651 915.166019881 0.00471683201946947 TRUE -"Methamidophos" NA NA NA 114 NA "10" -0.0808744594898649 205.122636803 0.00105721694225077 FALSE -"Methamidophos" NA NA NA 124 NA "10" -0.178837358040908 522.942952646 0.00269528589328229 FALSE -"Methamidophos" NA NA NA 125 NA "10" 0.944616104231969 4800.928386691 0.0247443329904978 TRUE -"Methamidophos" NA NA NA 142 NA "10" 1 194021.3295923 1 TRUE -"Methamidophos" NA NA NA 143 NA "10" 0.462998313752461 215.166582594 0.0011089841670817 TRUE -"Metolachlor" NA NA NA 176 NA "2" 0.791796112912307 995.27586705 0.00140948787866654 TRUE -"Metolachlor" NA NA NA 196 NA "2" 0.390316117761383 165.330739505 0.000234137771263337 TRUE -"Metolachlor" NA NA NA 212 NA "2" 0.793947617278503 3303.57566825 0.00467845148748308 TRUE -"Metolachlor" NA NA NA 220 NA "2" 0.784265545338331 134.73387814 0.000190807166506454 TRUE -"Metolachlor" NA NA NA 222 NA "2" 0.837765555939223 149.329081531 0.000211476573800797 TRUE -"Metolachlor" NA NA NA 224 NA "2" 0.333881608192525 1240.410666011 0.0017566424106045 TRUE -"Metolachlor" NA NA NA 238 NA "2" 0.0957538782410419 278.464510935 0.000394355339856714 TRUE -"Metolachlor" NA NA NA 240 NA "2" 0.702714684679668 309.572997085 0.000438410496425569 TRUE -"Metolachlor" NA NA NA 241 NA "2" 0.310895385493475 198.540365455 0.000281168515985718 TRUE -"Metolachlor" NA NA NA 243 NA "2" 0.131240121206885 350.776814924 0.000496762440566436 TRUE -"Metolachlor" NA NA NA 248 NA "2" 0.61859332075056 330.1702237165 0.000467579837542316 TRUE -"Metolachlor" NA NA NA 252 NA "2" 0.917041451436126 706125.8788487 1 TRUE -"Metolachlor" NA NA NA 253 NA "2" 0.855704337813672 610.27153687 0.000864253180842224 TRUE -"Metolachlor" NA NA NA 256 NA "2" 0.912087870841402 160.856989391 0.000227802144361666 TRUE -"Metolachlor" NA NA NA 266 NA "2" -0.228646021214337 2686.12464523 0.00380403087564158 FALSE -"Metolachlor" NA NA NA 267 NA "2" -0.172706372060116 90.919785974 0.000128758609048913 FALSE -"Metolachlor" NA NA NA 284 NA "2" 1 27717.1231987 0.0392523826543382 TRUE -"Metolachlor" NA NA NA 285 NA "2" 0.516690728602645 786.727229625 0.00111414586717558 TRUE -"Metolachlor" NA NA NA 105 NA "6" 0.147510907385547 67.732931137 0.000302088164521329 TRUE -"Metolachlor" NA NA NA 212 NA "6" 0.56820247221881 1215.116215726 0.00541940561447594 TRUE -"Metolachlor" NA NA NA 224 NA "6" -0.111227845735124 339.173356055 0.00151270962093686 FALSE -"Metolachlor" NA NA NA 252 NA "6" 0.993045070992658 224215.7723866 1 TRUE -"Metolachlor" NA NA NA 266 NA "6" -0.146787460104817 628.791106722 0.00280440176009482 FALSE -"Metolachlor" NA NA NA 284 NA "6" 1 155026.670419 0.691417328802802 TRUE -"Metolachlor" NA NA NA 285 NA "6" 0.118321686070868 459.575310689 0.00204970107944318 TRUE -"N,N-diethyl-m-toluamide ou DEET" NA NA NA 72 NA "1" 0.831213054372806 1933.43451305 0.00181816864864583 TRUE -"N,N-diethyl-m-toluamide ou DEET" NA NA NA 91 NA "1" 0.822308544953969 1277.57458017 0.00120140921882462 TRUE -"N,N-diethyl-m-toluamide ou DEET" NA NA NA 100 NA "1" 0.904831380805312 4819.97843154 0.0045326250318924 TRUE -"N,N-diethyl-m-toluamide ou DEET" NA NA NA 119 NA "1" 0.996276922706082 196757.537712 0.185027413154208 TRUE -"N,N-diethyl-m-toluamide ou DEET" NA NA NA 159 NA "1" 0.318506076968014 5745.2918091 0.00540277385870641 TRUE -"N,N-diethyl-m-toluamide ou DEET" NA NA NA 160 NA "1" -0.60812844929883 81418.296387 0.076564369218524 FALSE -"N,N-diethyl-m-toluamide ou DEET" NA NA NA 174 NA "1" -0.0254778159834255 6464.1887357 0.00607881219604324 FALSE -"N,N-diethyl-m-toluamide ou DEET" NA NA NA 178 NA "1" 0.189033868824133 1156.2770652 0.00108734311656538 TRUE -"N,N-diethyl-m-toluamide ou DEET" NA NA NA 192 NA "1" 1 1063396.68462 1 TRUE -"N,N-diethyl-m-toluamide ou DEET" NA NA NA 193 NA "1" 0.843516913487705 669.860601479 0.000629925418394897 TRUE -"Nigericin" NA NA NA 303 NA "8" 0.69388156788724 256.771903521 2.6267948084131e-05 TRUE -"Nigericin" NA NA NA 345 NA "8" 0.488441108859454 170.187350269 1.74102867959473e-05 TRUE -"Nigericin" NA NA NA 361 NA "8" -0.298158261851774 270.481686601 2.76704686296107e-05 FALSE -"Nigericin" NA NA NA 377 NA "8" 0.921913240362568 212.930380819 2.17829291764015e-05 TRUE -"Nigericin" NA NA NA 399 NA "8" -0.00219607480717936 155.459186543 1.59035851871495e-05 TRUE -"Nigericin" NA NA NA 419 NA "8" -0.128312924215981 334.087566385 3.41773953030539e-05 FALSE -"Nigericin" NA NA NA 485 NA "8" -0.153312907002539 192.458596704 1.96886511228122e-05 FALSE -"Nigericin" NA NA NA 491 NA "8" -0.422922944471844 124.569573874 1.27435558739663e-05 FALSE -"Nigericin" NA NA NA 501 NA "8" 0.330721867433802 1962.279740704 0.000200742611043264 TRUE -"Nigericin" NA NA NA 502 NA "8" 0.746783956260905 200.27525187 2.04883004975159e-05 TRUE -"Nigericin" NA NA NA 507 NA "8" -0.354836880533629 218.69433498 2.23725857805091e-05 FALSE -"Nigericin" NA NA NA 509 NA "8" -0.728921794848418 199.1876421 2.03770372456477e-05 FALSE -"Nigericin" NA NA NA 523 NA "8" 0.0880948030696946 240.14782524 2.45672930699186e-05 TRUE -"Nigericin" NA NA NA 525 NA "8" 0.117962948439402 576.361316696 5.89621720175225e-05 TRUE -"Nigericin" NA NA NA 559 NA "8" 0.84810344800213 103.529180519 1.05911086913109e-05 TRUE -"Nigericin" NA NA NA 567 NA "8" -0.752351991905382 249.41364288 2.55151927948768e-05 FALSE -"Nigericin" NA NA NA 568 NA "8" -0.532840101817629 259.228322029 2.65192414419954e-05 FALSE -"Nigericin" NA NA NA 573 NA "8" 0.244836394250901 221.88957263 2.26994608612938e-05 TRUE -"Nigericin" NA NA NA 580 NA "8" 0.992118727855313 194.64446546 1.99122670489084e-05 TRUE -"Nigericin" NA NA NA 583 NA "8" -0.188987118257525 7100.821918505 0.000726419125115431 FALSE -"Nigericin" NA NA NA 589 NA "8" -0.259152968299446 295.832520469 3.0263876937929e-05 FALSE -"Nigericin" NA NA NA 597 NA "8" -0.0565070203738975 733.689611459 7.50569683029789e-05 FALSE -"Nigericin" NA NA NA 599 NA "8" 0.972283168725802 643.235493679 6.58034478154985e-05 TRUE -"Nigericin" NA NA NA 605 NA "8" 0.429575707714564 667.355635634 6.82709554671057e-05 TRUE -"Nigericin" NA NA NA 607 NA "8" 0.386766245051255 160.19072342 1.63876247699032e-05 TRUE -"Nigericin" NA NA NA 641 NA "8" -0.367379921280677 128.127842899 1.31075693222306e-05 FALSE -"Nigericin" NA NA NA 643 NA "8" -0.327136371457191 200.36151887 2.04971256728809e-05 FALSE -"Nigericin" NA NA NA 649 NA "8" 0.0943387745709055 318.911627299 3.26248859569277e-05 TRUE -"Nigericin" NA NA NA 659 NA "8" -0.44098780723767 191.511249542 1.95917368353539e-05 FALSE -"Nigericin" NA NA NA 662 NA "8" 0.545210082812083 564.714775576 5.77707225898213e-05 TRUE -"Nigericin" NA NA NA 663 NA "8" 0.781327728555262 298.1920786 3.05052614104381e-05 TRUE -"Nigericin" NA NA NA 665 NA "8" 0.175836851592496 7548.058466541 0.000772171741597377 TRUE -"Nigericin" NA NA NA 666 NA "8" 0.677134729766668 281.057827949 2.87524154004613e-05 TRUE -"Nigericin" NA NA NA 669 NA "8" 0.492874926182605 356.941339497 3.65153525226741e-05 TRUE -"Nigericin" NA NA NA 673 NA "8" 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0.0989973953137751 FALSE +"Chlorfenvinphos" NA NA NA 287.097 NA "6" -0.246131897006268 1436.521243097 0.0193071513614688 FALSE +"Chlorfenvinphos" NA NA NA 299.097 NA "6" 0.0508805989280348 4075.071828875 0.054769833016409 TRUE +"Chlorfenvinphos" NA NA NA 301.175 NA "6" 0.449299997298531 184.163766389 0.00247520023115349 TRUE +"Chlorfenvinphos" NA NA NA 303.002 NA "6" 0.469612773913552 558.96223402 0.00751257143563184 TRUE +"Chlorfenvinphos" NA NA NA 315.15 NA "6" -0.535392132745364 228.835577496 0.00307559888364704 FALSE +"Chlorfenvinphos" NA NA NA 317.058 NA "6" 0.108398080800289 371.096517574 0.00498761620751847 TRUE +"Chlorfenvinphos" NA NA NA 327.106 NA "6" -0.0292180991930868 857.215583061 0.0115211599487992 FALSE +"Chlorfenvinphos" NA NA NA 331.034 NA "6" 0.935671136523579 10942.34945269 0.147067506414108 TRUE +"Chlorfenvinphos" NA NA NA 341.156 NA "6" 0.3027544679085 681.509114277 0.0091596275981267 TRUE +"Chlorfenvinphos" NA NA NA 359.083 NA "6" 0.963091521050382 70775.23458992 0.951234221865785 TRUE +"Chlorfenvinphos" NA NA NA 359.907 NA "6" 0.316260785934268 336.06626725 0.0045168021847634 TRUE +"Chlormequat" NA NA NA 103.875 NA "3" 0.258848039085982 1344.00603488 0.0035075545862099 TRUE +"Chlormequat" NA NA NA 121.939 NA "3" 1 383174.65968 1 TRUE +"Chlormequat" NA NA NA 103.891 NA "7" -0.238480528781348 249.84195518 0.00659545474896182 FALSE +"Chlormequat" NA NA NA 121.989 NA "7" 1 37880.9293202 1 TRUE +"Desisopropylatrazine" NA NA NA 78.873 NA "1" -0.00233999251843864 530.25218964 0.0010623465213357 TRUE +"Desisopropylatrazine" NA NA NA 114.851 NA "1" 0.0134526232413478 19215.13916 0.0384970333785257 TRUE +"Desisopropylatrazine" NA NA NA 129.922 NA "1" 0.263395383425939 3994.6477049 0.00800317316208218 TRUE +"Desisopropylatrazine" NA NA NA 131.851 NA "1" -0.0312768712385 7326.0765379 0.0146776045005323 FALSE +"Desisopropylatrazine" NA NA NA 132.89 NA "1" 0.249785689081156 9816.328859 0.0196667604950881 TRUE +"Desisopropylatrazine" NA NA NA 141.94 NA "1" 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0.000421677333233239 TRUE +"Dichlorvos" NA NA NA 108.907 NA "8" 0.967088540122942 63244.728942055 0.138018305315196 TRUE +"Dichlorvos" NA NA NA 111.003 NA "8" 0.669971084873578 362.689319128 0.000791493078068717 TRUE +"Dichlorvos" NA NA NA 116.962 NA "8" 0.427724412537125 150.021759756 0.000327390904954265 TRUE +"Dichlorvos" NA NA NA 119.018 NA "8" 0.352320220252662 842.015996927 0.00183752263450484 TRUE +"Dichlorvos" NA NA NA 121.012 NA "8" 0.347913703205373 778.073791986 0.00169798223466916 TRUE +"Dichlorvos" NA NA NA 123.095 NA "8" 0.375380270767784 270.12158084 0.000589483478548166 TRUE +"Dichlorvos" NA NA NA 126.93 NA "8" 0.948284758535013 7147.09441171 0.0155970287980156 TRUE +"Dichlorvos" NA NA NA 133.034 NA "8" 0.111433255667834 852.743870701 0.00186093396036062 TRUE +"Dichlorvos" NA NA NA 135.079 NA "8" 0.0748728027193132 220.929068083 0.000482131176490902 TRUE +"Dichlorvos" NA NA NA 136.984 NA "8" 0.453769927098964 505.667025571 0.00110351181972854 TRUE +"Dichlorvos" NA NA NA 138.985 NA "8" 0.467524552074558 137.935647968 0.000301015510597557 TRUE +"Dichlorvos" NA NA NA 143.009 NA "8" 0.278796612798532 266.444155698 0.000581458272424074 TRUE +"Dichlorvos" NA NA NA 144.921 NA "8" 0.994170372012309 44316.40897363 0.0967112321692371 TRUE +"Dichlorvos" NA NA NA 145.872 NA "8" 0.346301417994264 207.562618724 0.000452961714948885 TRUE +"Dichlorvos" NA NA NA 147.046 NA "8" -0.183799172220307 819.102781302 0.00178751936557185 FALSE +"Dichlorvos" NA NA NA 148.978 NA "8" 0.291827272614207 273.867382537 0.000597657902107486 TRUE +"Dichlorvos" NA NA NA 151.105 NA "8" -0.0612144593206886 544.88402842 0.00118909467166422 FALSE +"Dichlorvos" NA NA NA 153.072 NA "8" 0.459453598609755 595.225358962 0.00129895402666414 TRUE +"Dichlorvos" NA NA NA 157.075 NA "8" -0.0788899965991259 259.340542296 0.000565956131775221 FALSE +"Dichlorvos" NA NA NA 158.986 NA "8" 0.0596826580176188 1143.682675356 0.00249584664700842 TRUE +"Dichlorvos" NA NA NA 160.95 NA "8" 0.106726535917086 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0.00144343334318478 FALSE +"Fluopyram" NA NA NA 317.175 NA "2" 0.747044352703202 276.576972023 0.000239692511957673 TRUE +"Fluopyram" NA NA NA 319.208 NA "2" 0.411135022271651 205.162689204 0.000177802077937308 TRUE +"Fluopyram" NA NA NA 321.075 NA "2" 0.668663039963109 172.5105753 0.000149504468251542 TRUE +"Fluopyram" NA NA NA 322.207 NA "2" 0.457450301072192 363.92931174 0.000315395494671673 TRUE +"Fluopyram" NA NA NA 323.148 NA "2" 0.525525654158042 541.443225855 0.000469236053668481 TRUE +"Fluopyram" NA NA NA 325.172 NA "2" -0.375139543472427 284.063552627 0.000246180677974607 FALSE +"Fluopyram" NA NA NA 335.143 NA "2" 0.85099649332553 354.179540117 0.000306945958059 TRUE +"Fluopyram" NA NA NA 337.149 NA "2" -0.0800505936255548 6092.33305747 0.00527985610496276 FALSE +"Fluopyram" NA NA NA 339.165 NA "2" 0.0817418256376614 1257.39245224 0.001089705889791 TRUE +"Fluopyram" NA NA NA 351.264 NA "2" 0.0922108519959764 325.871292118 0.000282412913885544 TRUE +"Fluopyram" NA NA NA 353.206 NA "2" 0.73819712073071 219.68107702 0.000190384285413725 TRUE +"Fluopyram" NA NA NA 355.042 NA "2" 0.558938657015514 404.386810763 0.0003504575589405 TRUE +"Fluopyram" NA NA NA 357.092 NA "2" 0.962259996620823 6087.032030074 0.00527526202555257 TRUE +"Fluopyram" NA NA NA 361.224 NA "2" 0.552153478272702 857.635546693 0.000743260789310912 TRUE +"Fluopyram" NA NA NA 365.223 NA "2" -0.00936270431495669 3128.58431621 0.00271135455760717 FALSE +"Fluopyram" NA NA NA 377.099 NA "2" 0.95522089194523 6353.409628619 0.00550611535819805 TRUE +"Fluopyram" NA NA NA 379.135 NA "2" 0.976200924337964 23757.38885012 0.0205890901523317 TRUE +"Fluopyram" NA NA NA 380.163 NA "2" 0.802086185702225 299.634428489 0.000259675013101082 TRUE +"Fluopyram" NA NA NA 383.011 NA "2" 0.514484227137365 296.36061955 0.000256837801157807 TRUE +"Fluopyram" NA NA NA 397.143 NA "2" 1 1153882.4044359 1 TRUE +"Fluopyram" NA NA NA 397.852 NA "2" 0.629183355208795 786.96763037 0.000682017185932154 TRUE +"Hydroxy-tebuconazole" NA NA NA 104.943 NA "3" 0.933250800122397 148.864868642 0.000349259198550838 TRUE +"Hydroxy-tebuconazole" NA NA NA 111.016 NA "3" -0.136986211620653 819.476129504 0.00192261329911496 FALSE +"Hydroxy-tebuconazole" NA NA NA 124.953 NA "3" 0.937808762193969 1183.686924417 0.00277710617910255 TRUE +"Hydroxy-tebuconazole" NA NA NA 128.989 NA "3" 0.93947878913899 361.506768723 0.000848148830994743 TRUE +"Hydroxy-tebuconazole" NA NA NA 130.031 NA "3" 0.688489556152789 331.007312771 0.000776592555567199 TRUE +"Hydroxy-tebuconazole" NA NA NA 138.998 NA "3" 0.773254709339752 1538.894389073 0.00361047590264274 TRUE +"Hydroxy-tebuconazole" NA NA NA 142.055 NA "3" 0.570848007480712 609.52418229 0.00143003469754783 TRUE +"Hydroxy-tebuconazole" NA NA NA 143.052 NA "3" 0.806393964441417 697.26483626 0.00163588736624957 TRUE +"Hydroxy-tebuconazole" NA NA NA 144.028 NA "3" 0.617078750669289 821.504440261 0.00192737201885766 TRUE +"Hydroxy-tebuconazole" NA NA NA 150.967 NA "3" 0.969913176100367 8918.60934376 0.020924388541131 TRUE +"Hydroxy-tebuconazole" NA NA NA 163.01 NA "3" 0.943479253411026 4190.003754782 0.00983037412836093 TRUE +"Hydroxy-tebuconazole" NA NA NA 165.016 NA "3" 0.974027692942281 11141.070391724 0.0261386138415883 TRUE +"Hydroxy-tebuconazole" NA NA NA 177.025 NA "3" 0.976181868104272 5276.840125508 0.0123802544544473 TRUE +"Hydroxy-tebuconazole" NA NA NA 179.05 NA "3" 0.985734009124796 18898.49200271 0.0443386826650093 TRUE +"Hydroxy-tebuconazole" NA NA NA 181.003 NA "3" 0.815011717512525 2102.659529777 0.00493315305951243 TRUE +"Hydroxy-tebuconazole" NA NA NA 183.071 NA "3" 0.629817289150805 328.86962314 0.000771577216662296 TRUE +"Hydroxy-tebuconazole" NA NA NA 191.055 NA "3" 0.627994719460226 789.382863066 0.00185201000490732 TRUE +"Hydroxy-tebuconazole" NA NA NA 193.087 NA "3" 0.834581905027916 786.770006146 0.00184587985262806 TRUE +"Hydroxy-tebuconazole" NA NA NA 207.094 NA "3" 0.912806973260801 1817.33848199 0.00426374729985384 TRUE +"Hydroxy-tebuconazole" NA NA NA 213.136 NA "3" 0.533276651096227 209.824030864 0.000492278490719679 TRUE +"Hydroxy-tebuconazole" NA NA NA 219.028 NA "3" 0.973387546070147 5785.704654759 0.0135741265834354 TRUE +"Hydroxy-tebuconazole" NA NA NA 225.246 NA "3" 0.158710766132164 598.46658039 0.00140409191324474 TRUE +"Hydroxy-tebuconazole" NA NA NA 233.996 NA "3" 0.533892369953371 498.037124195 0.00116846942083577 TRUE +"Hydroxy-tebuconazole" NA NA NA 236.081 NA "3" 0.757916887845443 401.455109619 0.000941873600660352 TRUE +"Hydroxy-tebuconazole" NA NA NA 237.098 NA "3" 0.819617372910582 1804.698136231 0.00423409116224753 TRUE +"Hydroxy-tebuconazole" NA NA NA 241.966 NA "3" 0.0281666681525705 492.2943644595 0.00115499604944205 TRUE +"Hydroxy-tebuconazole" NA NA NA 249.215 NA "3" 0.148844380563395 668.821608301 0.00156915530856678 TRUE +"Hydroxy-tebuconazole" NA NA NA 251.196 NA "3" -0.0957358039667109 294.37336396 0.000690643844375629 FALSE +"Hydroxy-tebuconazole" NA NA NA 252.021 NA "3" 0.571270701114537 262.84086132 0.000616663887245291 TRUE +"Hydroxy-tebuconazole" NA NA NA 260.974 NA "3" 0.307249106849353 301.249457372 0.000706776185714076 TRUE +"Hydroxy-tebuconazole" NA NA NA 262.007 NA "3" -0.0664296147654578 356.3203392 0.000835980693306733 FALSE +"Hydroxy-tebuconazole" NA NA NA 264.108 NA "3" -0.234448577231542 1060.76663015 0.00248871682402531 FALSE +"Hydroxy-tebuconazole" NA NA NA 266.097 NA "3" 0.442854013871549 224.958957681 0.000527787287781417 TRUE +"Hydroxy-tebuconazole" NA NA NA 268.218 NA "3" 0.333877814717464 167.482578998 0.00039293912556858 TRUE +"Hydroxy-tebuconazole" NA NA NA 276.183 NA "3" 0.814390714374443 472.387895585 0.00110829250260451 TRUE +"Hydroxy-tebuconazole" NA NA NA 278.186 NA "3" 0.275231308762053 379.986748698 0.000891505621983662 TRUE +"Hydroxy-tebuconazole" NA NA NA 280.045 NA "3" 0.650641022624376 416.402436187 0.000976942259540319 TRUE +"Hydroxy-tebuconazole" NA NA NA 282.042 NA "3" 0.782140125615591 155.801819332 0.000365534320145864 TRUE +"Hydroxy-tebuconazole" NA NA NA 288.14 NA "3" 0.702501554923525 901.789572159 0.00211573292011017 TRUE +"Hydroxy-tebuconazole" NA NA NA 292.107 NA "3" -0.282700274468723 1574.001168335 0.00369284164615631 FALSE +"Hydroxy-tebuconazole" NA NA NA 296.201 NA "3" -0.00403563274731662 354.472442154 0.000831645251055126 TRUE +"Hydroxy-tebuconazole" NA NA NA 306.19 NA "3" 0.939487898745732 6832.34144213 0.0160296926875516 TRUE +"Hydroxy-tebuconazole" NA NA NA 307.097 NA "3" 0.647420935806109 170.978830823 0.000401141854133558 TRUE +"Hydroxy-tebuconazole" NA NA NA 324.177 NA "3" 1 426230.3448547 1 TRUE +"Hydroxy-tebuconazole" NA NA NA 325.033 NA "3" 0.526687588803207 740.769098256 0.0017379548575044 TRUE +"Isoproturon" NA NA NA 71.89 NA "2" 0.993086605464471 59907.1442268 0.115787147683237 TRUE +"Isoproturon" NA NA NA 119.978 NA "2" 0.927282017838371 790.062006494 0.00152701363761405 TRUE +"Isoproturon" NA NA NA 133.985 NA "2" 0.71269989274101 432.2311039 0.000835406315999436 TRUE +"Isoproturon" NA NA NA 137.024 NA "2" 0.213034502535958 770.65881154 0.00148951158959186 TRUE +"Isoproturon" NA NA NA 146.925 NA "2" -0.543816345969317 1151.6802063 0.00222594095999428 FALSE +"Isoproturon" NA NA NA 149.063 NA "2" 0.500520723996853 390.29506684 0.000754353310068573 TRUE +"Isoproturon" NA NA NA 161.063 NA "2" 0.400505614578046 614.84665681 0.00118836144792821 TRUE +"Isoproturon" NA NA NA 162.055 NA "2" 0.804730923860733 2048.22309885 0.00395875840011529 TRUE +"Isoproturon" NA NA NA 165.029 NA "2" 0.985177338187729 41795.7801207 0.0807819205510825 TRUE +"Isoproturon" NA NA NA 173.91 NA "2" -0.672244697055266 2538.22496785 0.00490582271945875 FALSE +"Isoproturon" NA NA NA 174.904 NA "2" -0.891117335203028 41310.6113296 0.0798441974933163 FALSE +"Isoproturon" NA NA NA 179.091 NA "2" 0.106337033555785 305.46005153 0.000590386147667693 TRUE +"Isoproturon" NA NA NA 189.09 NA "2" -0.557815616548336 2256.78026215 0.00436185287873026 FALSE +"Isoproturon" NA NA NA 192.871 NA "2" -0.457037805653279 900.73918538 0.00174092793819098 FALSE +"Isoproturon" NA NA NA 207.103 NA "2" 1 517390.275393 1 TRUE +"Malathion dicarboxilic acid" NA NA NA 98.901 NA "5" -0.0145062980310714 146.313006405 0.00728513388971739 FALSE +"Malathion dicarboxilic acid" NA NA NA 101.001 NA "5" -0.0828141093237674 435.762945656 0.0216972604232751 FALSE +"Malathion dicarboxilic acid" NA NA NA 104.913 NA "5" 0.587019603923614 89.451040273 0.00445389525494049 TRUE +"Malathion dicarboxilic acid" NA NA NA 110.87 NA "5" -0.390287162095832 129.625732421 0.00645425064690212 FALSE +"Malathion dicarboxilic acid" NA NA NA 112.962 NA "5" 0.436063164175773 214.697242755 0.0106900828412605 TRUE +"Malathion dicarboxilic acid" NA NA NA 114.854 NA "5" -0.487491202047035 169.733005041 0.00845124912412097 FALSE +"Malathion dicarboxilic acid" NA NA NA 124.899 NA "5" 0.211743045350572 976.859200016 0.0486392169662613 TRUE +"Malathion dicarboxilic acid" NA NA NA 126.97 NA "5" -0.193115673489529 251.457530026 0.0125204301300888 FALSE +"Malathion dicarboxilic acid" NA NA NA 132.921 NA "5" -0.0235937319440911 106.381536014 0.00529688885696561 FALSE +"Malathion dicarboxilic acid" NA NA NA 134.959 NA "5" 0.0943867349562522 265.367501262 0.0132130274961485 TRUE +"Malathion dicarboxilic acid" NA NA NA 142.949 NA "5" 0.324562260639024 2027.15360119 0.100934877647263 TRUE +"Malathion dicarboxilic acid" NA NA NA 144.918 NA "5" 0.0513679474641989 340.208190446 0.0169394524702548 TRUE +"Malathion dicarboxilic acid" NA NA NA 154.962 NA "5" -0.0935008127275434 89.39838505 0.00445127347606401 FALSE +"Malathion dicarboxilic acid" NA NA NA 156.946 NA "5" -0.124840593853139 283.279369826 0.014104885054885 FALSE +"Malathion dicarboxilic acid" NA NA NA 158.921 NA "5" 0.615282973488168 11570.4075283 0.576107142306516 TRUE +"Malathion dicarboxilic acid" NA NA NA 170.98 NA "5" -0.157617624578159 343.725625045 0.0171145905706306 FALSE +"Malathion dicarboxilic acid" NA NA NA 173.045 NA "5" 0.13521369536174 276.705667733 0.0137775710239911 TRUE +"Malathion dicarboxilic acid" NA NA NA 173.932 NA "5" 0.0546754802243834 145.849533325 0.00726205690206577 TRUE +"Malathion dicarboxilic acid" NA NA NA 174.978 NA "5" -0.0449871685056207 1172.409335654 0.0583759379542223 FALSE +"Malathion dicarboxilic acid" NA NA NA 177.077 NA "5" 0.124276700228139 180.05658699 0.00896527503724966 TRUE +"Malathion dicarboxilic acid" NA NA NA 183.054 NA "5" 0.118394234041897 92.657263754 0.00461353770856342 TRUE +"Malathion dicarboxilic acid" NA NA NA 184.956 NA "5" -0.074153926813293 212.018755439 0.0105567171262197 FALSE +"Malathion dicarboxilic acid" NA NA NA 187.004 NA "5" 0.108830633613764 941.066299451 0.0468570372453718 TRUE +"Malathion dicarboxilic acid" NA NA NA 189.021 NA "5" 0.508419430479885 146.580297463 0.00729844269385517 TRUE +"Malathion dicarboxilic acid" NA NA NA 189.911 NA "5" 0.87690485484064 148.989129555 0.0074183818895511 TRUE +"Malathion dicarboxilic acid" NA NA NA 192.981 NA "5" -0.0384696232288205 1596.369196382 0.0794855058946147 FALSE +"Malathion dicarboxilic acid" NA NA NA 197.022 NA "5" -0.0619440037636622 179.884572989 0.00895671021407378 FALSE +"Malathion dicarboxilic acid" NA NA NA 198.997 NA "5" -0.028668865104496 276.667024113 0.0137756469028716 FALSE +"Malathion dicarboxilic acid" NA NA NA 201.02 NA "5" 0.237137284012593 239.864170096 0.0119431801548682 TRUE +"Malathion dicarboxilic acid" NA NA NA 202.991 NA "5" -0.0966182688129124 1407.858670707 0.0700992971568763 FALSE +"Malathion dicarboxilic acid" NA NA NA 205.027 NA "5" 0.133069171499041 130.40357304 0.00649298044402344 TRUE +"Malathion dicarboxilic acid" NA NA NA 213.08 NA "5" -0.457317913367628 282.143243319 0.0140483156908721 FALSE +"Malathion dicarboxilic acid" NA NA NA 215.035 NA "5" 0.104159055038702 4632.372268515 0.23065244185969 TRUE +"Malathion dicarboxilic acid" NA NA NA 215.963 NA "5" 0.149064407342261 152.968408575 0.00761651588431708 TRUE +"Malathion dicarboxilic acid" NA NA NA 217.11 NA "5" -0.065462150775907 149.235903278 0.00743066910622917 FALSE +"Malathion dicarboxilic acid" NA NA NA 219.11 NA "5" 0.135712941972458 275.246332175 0.0137049086189782 TRUE +"Malathion dicarboxilic acid" NA NA NA 229.034 NA "5" 0.1770967268039 508.844859597 0.0253361134621037 TRUE +"Malathion dicarboxilic acid" NA NA NA 231.032 NA "5" -0.102884748154224 548.515546309 0.027311373702427 FALSE +"Malathion dicarboxilic acid" NA NA NA 233.021 NA "5" 0.0252727083027678 5883.46527449 0.292946152316215 TRUE +"Malathion dicarboxilic acid" NA NA NA 239.07 NA "5" 0.360021753339356 289.00519777 0.0143899822190159 TRUE +"Malathion dicarboxilic acid" NA NA NA 243 NA "5" -0.053037039486054 3332.41069708 0.165925495622409 FALSE +"Malathion dicarboxilic acid" NA NA NA 244.961 NA "5" -0.281228966283381 369.79291249 0.0184125181017819 FALSE +"Malathion dicarboxilic acid" NA NA NA 247.121 NA "5" -0.000759194687357852 453.035788533 0.0225572999789294 TRUE +"Malathion dicarboxilic acid" NA NA NA 256.992 NA "5" 1 20083.7772675 1 TRUE +"Malathion dicarboxilic acid" NA NA NA 261.023 NA "5" -0.0148073154145046 138.486630433 0.00689544743443765 FALSE +"Malathion dicarboxilic acid" NA NA NA 275.072 NA "5" 0.106470337603423 7538.973325 0.375376266356017 TRUE +"Methamidophos" NA NA NA 93.9 NA "10" 0.976908842717177 9354.73397623 0.0482149771671354 TRUE +"Methamidophos" NA NA NA 99.88 NA "10" 0.513584871583348 164.780854231 0.000849292469942643 TRUE +"Methamidophos" NA NA NA 109.875 NA "10" 0.284212959905891 434.336410282 0.0022386013496283 TRUE +"Methamidophos" NA NA NA 111.944 NA "10" 0.703154152581651 915.166019881 0.00471683201946947 TRUE +"Methamidophos" NA NA NA 114.009 NA "10" -0.0808744594898649 205.122636803 0.00105721694225077 FALSE +"Methamidophos" NA NA NA 123.965 NA "10" -0.178837358040908 522.942952646 0.00269528589328229 FALSE +"Methamidophos" NA NA NA 124.905 NA "10" 0.944616104231969 4800.928386691 0.0247443329904978 TRUE +"Methamidophos" NA NA NA 141.916 NA "10" 1 194021.3295923 1 TRUE +"Methamidophos" NA NA NA 142.955 NA "10" 0.462998313752461 215.166582594 0.0011089841670817 TRUE +"Metolachlor" NA NA NA 176.128 NA "2" 0.760582065871439 995.27586705 0.00140948787866654 TRUE +"Metolachlor" NA NA NA 196.04 NA "2" 0.191220558744757 165.330739505 0.000234137771263337 TRUE +"Metolachlor" NA NA NA 212.064 NA "2" 0.931185345473568 3303.57566825 0.00467845148748308 TRUE +"Metolachlor" NA NA NA 220.094 NA "2" 0.643787158940323 134.73387814 0.000190807166506454 TRUE +"Metolachlor" NA NA NA 222.125 NA "2" 0.424376972972785 149.329081531 0.000211476573800797 TRUE +"Metolachlor" NA NA NA 224.025 NA "2" 0.280374162629315 1240.410666011 0.0017566424106045 TRUE +"Metolachlor" NA NA NA 238.138 NA "2" 0.391062783784674 278.464510935 0.000394355339856714 TRUE +"Metolachlor" NA NA NA 240.107 NA "2" 0.591264299722738 309.572997085 0.000438410496425569 TRUE +"Metolachlor" NA NA NA 241.023 NA "2" 0.595274120987579 198.540365455 0.000281168515985718 TRUE +"Metolachlor" NA NA NA 243.012 NA "2" 0.396358480157969 350.776814924 0.000496762440566436 TRUE +"Metolachlor" NA NA NA 248.131 NA "2" 0.678240672160261 330.1702237165 0.000467579837542316 TRUE +"Metolachlor" NA NA NA 252.088 NA "2" 1 706125.8788487 1 TRUE +"Metolachlor" NA NA NA 253.149 NA "2" 0.617816316710038 610.27153687 0.000864253180842224 TRUE +"Metolachlor" NA NA NA 256.233 NA "2" 0.912395716840148 160.856989391 0.000227802144361666 TRUE +"Metolachlor" NA NA NA 266.126 NA "2" -0.116852848038893 2686.12464523 0.00380403087564158 FALSE +"Metolachlor" NA NA NA 267.137 NA "2" 0.0441030462799913 90.919785974 0.000128758609048913 TRUE +"Metolachlor" NA NA NA 284.143 NA "2" 0.917041451436126 27717.1231987 0.0392523826543382 TRUE +"Metolachlor" NA NA NA 285.045 NA "2" 0.46981332944969 786.727229625 0.00111414586717558 TRUE +"Metolachlor" NA NA NA 104.917 NA "6" 0.130410538297487 67.732931137 0.000302088164521329 TRUE +"Metolachlor" NA NA NA 212.095 NA "6" 0.585824508393064 1215.116215726 0.00541940561447594 TRUE +"Metolachlor" NA NA NA 224.037 NA "6" -0.121009816842564 339.173356055 0.00151270962093686 FALSE +"Metolachlor" NA NA NA 252.116 NA "6" 1 224215.7723866 1 TRUE +"Metolachlor" NA NA NA 266.193 NA "6" -0.192997823151521 628.791106722 0.00280440176009482 FALSE +"Metolachlor" NA NA NA 284.148 NA "6" 0.993045070992658 155026.670419 0.691417328802802 TRUE +"Metolachlor" NA NA NA 284.996 NA "6" 0.137649546667365 459.575310689 0.00204970107944318 TRUE +"N,N-diethyl-m-toluamide ou DEET" NA NA NA 71.924 NA "1" 0.831213054372806 1933.43451305 0.00181816864864583 TRUE +"N,N-diethyl-m-toluamide ou DEET" NA NA NA 90.956 NA "1" 0.822308544953969 1277.57458017 0.00120140921882462 TRUE +"N,N-diethyl-m-toluamide ou DEET" NA NA NA 99.971 NA "1" 0.904831380805312 4819.97843154 0.0045326250318924 TRUE +"N,N-diethyl-m-toluamide ou DEET" NA NA NA 118.961 NA "1" 0.996276922706082 196757.537712 0.185027413154208 TRUE +"N,N-diethyl-m-toluamide ou DEET" 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TRUE +"Nigericin" NA NA NA 399.234 NA "8" -0.160310017373442 155.459186543 1.59035851871495e-05 FALSE +"Nigericin" NA NA NA 419.123 NA "8" 0.454680561332234 334.087566385 3.41773953030539e-05 TRUE +"Nigericin" NA NA NA 485.072 NA "8" 0.625478626726129 192.458596704 1.96886511228122e-05 TRUE +"Nigericin" NA NA NA 491.181 NA "8" 0.789429377035226 124.569573874 1.27435558739663e-05 TRUE +"Nigericin" NA NA NA 501.074 NA "8" 0.518631975615399 1962.279740704 0.000200742611043264 TRUE +"Nigericin" NA NA NA 501.674 NA "8" -0.430131005779289 200.27525187 2.04883004975159e-05 FALSE +"Nigericin" NA NA NA 507.181 NA "8" -0.251490955631681 218.69433498 2.23725857805091e-05 FALSE +"Nigericin" NA NA NA 509.012 NA "8" -0.429865460317741 199.1876421 2.03770372456477e-05 FALSE +"Nigericin" NA NA NA 523.044 NA "8" 0.751433918824564 240.14782524 2.45672930699186e-05 TRUE +"Nigericin" NA NA NA 525.047 NA "8" 0.369620356347346 576.361316696 5.89621720175225e-05 TRUE +"Nigericin" NA NA NA 559.128 NA "8" 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1.63876247699032e-05 TRUE +"Nigericin" NA NA NA 641.29 NA "8" 0.525836751321722 128.127842899 1.31075693222306e-05 TRUE +"Nigericin" NA NA NA 643.054 NA "8" -0.122597010721492 200.36151887 2.04971256728809e-05 FALSE +"Nigericin" NA NA NA 649.15 NA "8" 0.0135917112326882 318.911627299 3.26248859569277e-05 TRUE +"Nigericin" NA NA NA 659.2 NA "8" -0.0208921009305321 191.511249542 1.95917368353539e-05 FALSE +"Nigericin" NA NA NA 662.044 NA "8" 0.641603671405639 564.714775576 5.77707225898213e-05 TRUE +"Nigericin" NA NA NA 662.839 NA "8" -0.770778338634856 298.1920786 3.05052614104381e-05 FALSE +"Nigericin" NA NA NA 665.097 NA "8" 0.173815491725012 7548.058466541 0.000772171741597377 TRUE +"Nigericin" NA NA NA 665.749 NA "8" 0.300790361762257 281.057827949 2.87524154004613e-05 TRUE +"Nigericin" NA NA NA 669.122 NA "8" 0.0967591317188712 356.941339497 3.65153525226741e-05 TRUE +"Nigericin" NA NA NA 673.1 NA "8" 0.367543680004672 302.894679066 3.09863407777965e-05 TRUE +"Nigericin" NA NA NA 685.782 NA "8" 0.989073483112958 2607.612306107 0.000266760590785424 TRUE +"Nigericin" NA NA NA 687.162 NA "8" 0.117209497383374 3219.00846012 0.00032930685154147 TRUE +"Nigericin" NA NA NA 687.93 NA "8" -0.295647504227922 432.271391383 4.4221670328409e-05 FALSE +"Nigericin" NA NA NA 689.222 NA "8" 0.0990170536326388 331.674744123 3.39305618721164e-05 TRUE +"Nigericin" NA NA NA 689.69 NA "8" -0.0874519018397863 218.260694507 2.2328224052159e-05 FALSE +"Nigericin" NA NA NA 697.766 NA "8" 0.978490404441732 785.784382825 8.03863004103169e-05 TRUE +"Nigericin" NA NA NA 701.101 NA "8" 0.731316939349366 315.705478664 3.22968946746288e-05 TRUE +"Nigericin" NA NA NA 703.314 NA "8" 0.989992321852776 2052.161657913 0.000209937595005967 TRUE +"Nigericin" NA NA NA 703.713 NA "8" 0.812645867594796 20306.616162854 0.00207738125478592 TRUE +"Nigericin" NA NA NA 704.813 NA "8" 0.599238844962928 318.047350886 3.25364698660871e-05 TRUE +"Nigericin" NA NA NA 705.992 NA "8" 0.120548202111509 253.04758263 2.58869474120484e-05 TRUE +"Nigericin" NA NA NA 711.315 NA "8" 0.151876467907261 280.26337147 2.86711419384535e-05 TRUE +"Nigericin" NA NA NA 715.256 NA "8" 0.480161788515133 1563.55045611 0.000159952322060259 TRUE +"Nigericin" NA NA NA 715.695 NA "8" 0.72775020990742 2603.190510313 0.000266308237935432 TRUE +"Nigericin" NA NA NA 717.092 NA "8" -0.391884247279159 379.933180811 3.88674342174119e-05 FALSE +"Nigericin" NA NA NA 729.441 NA "8" 0.804708938857451 21682.60615534 0.002218146008216 TRUE +"Nigericin" NA NA NA 729.694 NA "8" 0.786614968968642 859696.24143705 0.0879475360369561 TRUE +"Nigericin" NA NA NA 730.964 NA "8" 0.975276542575758 1660.164900783 0.000169836048363826 TRUE +"Nigericin" NA NA NA 732.111 NA "8" 0.177582057430054 456.192295545 4.66687958122979e-05 TRUE +"Nigericin" NA NA NA 738.222 NA "8" -0.112157886239301 289.26318264 2.95918290126186e-05 FALSE +"Nigericin" NA NA NA 747.371 NA "8" -0.0779329807538978 3244089.5208734 0.331872661868578 FALSE +"Nigericin" NA NA NA 747.847 NA "8" 1 9775103.20557247 1 TRUE +"Nigericin" NA NA NA 748.688 NA "8" 0.871801308846705 19038.053184765 0.00194760636122103 TRUE +"Omethoate" NA NA NA 87.929 NA "2" 0.868211031404848 429.379247656 0.00784836708858288 TRUE +"Omethoate" NA NA NA 124.897 NA "2" 0.63416703268722 307.230954691 0.00561569131846479 TRUE +"Omethoate" NA NA NA 140.943 NA "2" 0.28867995166299 2547.8089448 0.0465698796099839 TRUE +"Omethoate" NA NA NA 153.952 NA "2" 0.445002235355301 1394.67151636 0.0254923685486383 TRUE +"Omethoate" NA NA NA 154.898 NA "2" 0.903281466013988 3686.16078187 0.0673771336681627 TRUE +"Omethoate" NA NA NA 157.948 NA "2" -0.171952225299012 5749.6453247 0.10509433649563 FALSE +"Omethoate" NA NA NA 171.95 NA "2" -0.593063434599588 180.908488267 0.0033067183221149 FALSE +"Omethoate" NA NA NA 173.018 NA "2" 0.59156649019933 570.920797354 0.0104355206279798 TRUE +"Omethoate" NA NA NA 181.925 NA "2" 0.167929175305517 2353.4972763 0.0430181725530914 TRUE +"Omethoate" NA NA NA 182.907 NA "2" 1 54709.3736582 1 TRUE +"Omethoate" NA NA NA 195.97 NA "2" 0.967697478321254 12714.1094668 0.232393621360613 TRUE +"Omethoate" NA NA NA 214.033 NA "2" 0.989920907401226 20372.4348769 0.37237558236689 TRUE +"Prochloraz" NA NA NA 201.986 NA "1" 0.654532994188289 320.311538685 0.00111224181016321 TRUE +"Prochloraz" NA NA NA 238.099 NA "1" 0.419623954559818 257.66075992 0.000894694806181419 TRUE +"Prochloraz" NA NA NA 244.082 NA "1" 0.717875977812794 894.255809314 0.00310519160247456 TRUE +"Prochloraz" NA NA NA 245.134 NA "1" -0.306469344418807 179.53681564 0.000623419167595921 FALSE +"Prochloraz" NA NA NA 265.97 NA "1" 0.959110121105955 6848.746319913 0.0237814161659027 TRUE +"Prochloraz" NA NA NA 280.082 NA "1" 0.945296169467766 2133.000283721 0.00740657706676483 TRUE +"Prochloraz" NA NA NA 291.007 NA "1" -0.00151994503068215 389.368725297 0.00135203426521318 TRUE +"Prochloraz" NA NA NA 294.043 NA "1" 0.133059143955174 1008.16582397 0.00350072990064777 TRUE +"Prochloraz" NA NA NA 303.009 NA "1" 0.495070256706509 206.674549112 0.000717651557489022 TRUE +"Prochloraz" NA NA NA 308.012 NA "1" 1 287987.3205252 1 TRUE +"Prochloraz" NA NA NA 310.113 NA "1" 0.322378179260344 261.194522859 0.000906965356608971 TRUE +"Prochloraz" NA NA NA 315.053 NA "1" -0.154138467883504 338.202372563 0.00117436549618304 FALSE +"Prochloraz" NA NA NA 316.099 NA "1" -0.0399268222906899 2865.441486445 0.00994988765900984 FALSE +"Prochloraz" NA NA NA 318.151 NA "1" 0.092384504879909 199.611021524 0.000693124340196544 TRUE +"Prochloraz" NA NA NA 330.215 NA "1" 0.0921833864370504 276.492937091 0.000960087189209449 TRUE +"Prochloraz" NA NA NA 332.181 NA "1" 0.3876058495216 376.843055239 0.00130854044043243 TRUE +"Prochloraz" NA NA NA 333.889 NA "1" 0.847586588601703 113.467085369 0.000394000281547365 TRUE +"Prochloraz" NA NA NA 335.042 NA "1" -0.1360577095389 215.835879809 0.000749463134055284 FALSE +"Prochloraz" NA NA NA 340.17 NA "1" 0.393974584266385 381.260290641 0.00132387873863925 TRUE 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"7" 0.485699748004766 872.686310784 0.0057551997945598 TRUE +"Prochloraz" NA NA NA 266.002 NA "7" 0.963071423354662 4327.34904575 0.0285380417125085 TRUE +"Prochloraz" NA NA NA 280.094 NA "7" 0.73706774686317 1298.919650077 0.00856612738265254 TRUE +"Prochloraz" NA NA NA 293.094 NA "7" -0.0928829745817302 200.444505207 0.00132189328620453 FALSE +"Prochloraz" NA NA NA 294.038 NA "7" -0.131949255889773 1575.694126647 0.0103914022735398 FALSE +"Prochloraz" NA NA NA 304.076 NA "7" -0.195251390549766 809.598223213 0.00533914588820071 FALSE +"Prochloraz" NA NA NA 308.049 NA "7" 1 151634.4074812 1 TRUE +"Prochloraz" NA NA NA 310.076 NA "7" -0.143486884545167 105.641312124 0.000696684307201831 FALSE +"Prochloraz" NA NA NA 315.042 NA "7" 0.245421552872291 440.677309527 0.00290618281725825 TRUE +"Prochloraz" NA NA NA 316.046 NA "7" 0.202875988168563 2305.138855487 0.0152019511519692 TRUE +"Prochloraz" NA NA NA 333.982 NA "7" 0.674615895655882 201.20180177 0.00132688751261778 TRUE +"Prochloraz" NA NA NA 344.079 NA "7" -0.113070554769094 697.322455414 0.0045987086110417 FALSE +"Prochloraz" NA NA NA 358.19 NA "7" -0.564930888257682 305.289077308 0.00201332324489645 FALSE +"Prochloraz" NA NA NA 360.155 NA "7" -0.502928639051151 135.6890707 0.000894843544772799 FALSE +"Prochloraz" NA NA NA 375.87 NA "7" -0.181127485034532 375.156909479 0.00247408827396587 FALSE +"p-Toluenesulfonamide" NA NA NA 112.779 NA "5" 0.325044247148387 527.826451544 0.0576739280872289 TRUE +"p-Toluenesulfonamide" NA NA NA 127.908 NA "5" -0.0640430379042245 236.805536746 0.0258749925415739 FALSE +"p-Toluenesulfonamide" NA NA NA 128.987 NA "5" -0.277635803719822 209.208140355 0.0228595122635519 FALSE +"p-Toluenesulfonamide" NA NA NA 129.898 NA "5" 0.000709137026072913 354.06029941 0.038687049856979 TRUE +"p-Toluenesulfonamide" NA NA NA 130.911 NA "5" -0.578543677033297 318.10253716 0.0347580588257077 FALSE +"p-Toluenesulfonamide" NA NA NA 139.929 NA "5" 0.12887185625977 1235.91298662 0.135044305763544 TRUE 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NA "1" NA 1346.46130371094 0.0108563010474573 NA +"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA 205.034 NA "1" NA 1612.63024902344 0.0130023784667138 NA +"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA 217.015 NA "1" NA 124025.7890625 1 NA diff -r 78d5a12406c2 -r 77abacd33c31 test-data/smol/out-smol-delta-0.05mz.tsv --- a/test-data/smol/out-smol-delta-0.05mz.tsv Fri Aug 05 17:25:45 2022 +0000 +++ b/test-data/smol/out-smol-delta-0.05mz.tsv Fri Sep 30 16:18:56 2022 +0000 @@ -1,20 +1,20 @@ "compoundName" "inchikey" "elemcomposition" "fragment" "fragment_mz" "ppm" "fileid" "CorWithPrecursor" "AbsoluteIntensity" "relativeIntensity" "corValid" -"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C13H8O4" "229" 2.02930325023702 "1" NA 203723.75 0.932156767504374 NA -"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" NA "312" NA "1" NA 3981.51538085938 0.0182177900573243 NA -"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" NA "313" NA "1" NA 7264.93603515625 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